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Carey SB, Jenkins J, Lovell JT, Maumus F, Sreedasyam A, Payton AC, Shu S, Tiley GP, Fernandez-Pozo N, Healey A, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, McBreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JG, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, McDaniel SF. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. SCIENCE ADVANCES 2021; 7:7/27/eabh2488. [PMID: 34193417 PMCID: PMC8245031 DOI: 10.1126/sciadv.abh2488] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/14/2021] [Indexed: 05/19/2023]
Abstract
Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.
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Affiliation(s)
- Sarah B Carey
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Florian Maumus
- Université Paris-Saclay, INRAE, URGI, 78026 Versailles, France
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam C Payton
- Department of Biology, University of Florida, Gainesville, FL, USA
- RAPiD Genomics, Gainesville, FL, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Jordan C McBreen
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Leslie M Kollar
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
| | - Sanna Huttunen
- Department of Biology and Biodiversity Unit, University of Turku, Turku, Finland
| | - Jacob B Landis
- L.H. Bailey Hortorium and Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL, USA
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104 Freiburg im Breisgau, Germany
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Burtscher WP, List MA, Payton AC, McDaniel SF, Carey SB. Area from image analyses accurately estimates dry-weight biomass of juvenile tissue from the moss Ceratodon purpureus. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11418. [PMID: 33968498 PMCID: PMC8085951 DOI: 10.1002/aps3.11418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
PREMISE Mosses have long served as models for studying many areas of plant biology. Investigators have used two-dimensional measurements of juvenile growth from photographs as a surrogate for dry-weight biomass. The relationship between area and biomass, however, has not been critically evaluated. METHODS Here we grew axenic tissue cultures of 10 Ceratodon purpureus isolates to study the relationship between these parameters. We measured area and biomass on replicate cultures with two distinct starting inoculum sizes each week for three weeks. We then examined the correlation between area and biomass as well as the influence of variation in inoculum size on both parameters. RESULTS We found a strong correlation between area and biomass after two weeks of growth. Furthermore, we found inoculum size affected biomass during the first week of growth but not in subsequent weeks and inoculum size had no detectable effect on area. DISCUSSION These analyses provide experimental confirmation that area is a suitable proxy for biomass and provide clear guidelines for when inoculum size variation may affect downstream growth estimates.
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Affiliation(s)
| | - Marna A. List
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
| | - Adam C. Payton
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
| | | | - Sarah B. Carey
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
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Shortlidge EE, Carey SB, Payton AC, McDaniel SF, Rosenstiel TN, Eppley SM. Microarthropod contributions to fitness variation in the common moss Ceratodon purpureus. Proc Biol Sci 2021; 288:20210119. [PMID: 33784868 PMCID: PMC8059975 DOI: 10.1098/rspb.2021.0119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The evolution of sustained plant–animal interactions depends critically upon genetic variation in the fitness benefits from the interaction. Genetic analyses of such interactions are limited to a few model systems, in part because genetic variation may be absent or the interacting species may be experimentally intractable. Here, we examine the role of sperm-dispersing microarthropods in shaping reproduction and genetic variation in mosses. We established experimental mesocosms with known moss genotypes and inferred the parents of progeny from mesocosms with and without microarthropods, using a pooled sequencing approach. Moss reproductive rates increased fivefold in the presence of microarthropods, relative to control mesocosms. Furthermore, the presence of microarthropods increased the total number of reproducing moss genotypes, and changed the rank-order of fitness of male and female moss genotypes. Interestingly, the genotypes that reproduced most frequently did not produce sporophytes with the most spores, highlighting the challenge of defining fitness in mosses. These results demonstrate that microarthropods provide a fitness benefit for mosses, and highlight the potential for biotic dispersal agents to alter fitness among moss genotypes.
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Affiliation(s)
- Erin E Shortlidge
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97202-0751, USA
| | - Sarah B Carey
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA
| | - Adam C Payton
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA
| | - Todd N Rosenstiel
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97202-0751, USA
| | - Sarah M Eppley
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97202-0751, USA
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Biersma EM, Convey P, Wyber R, Robinson SA, Dowton M, van de Vijver B, Linse K, Griffiths H, Jackson JA. Latitudinal Biogeographic Structuring in the Globally Distributed Moss Ceratodon purpureus. FRONTIERS IN PLANT SCIENCE 2020; 11:502359. [PMID: 32983208 PMCID: PMC7484499 DOI: 10.3389/fpls.2020.502359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Biogeographic patterns of globally widespread species are expected to reflect regional structure, as well as connectivity caused by occasional long-distance dispersal. We assessed the level and drivers of population structure, connectivity, and timescales of population isolation in one of the most widespread and ruderal plants in the world - the common moss Ceratodon purpureus. We applied phylogenetic, population genetic, and molecular dating analyses to a global (n = 147) sampling data set, using three chloroplast loci and one nuclear locus. The plastid data revealed several distinct and geographically structured lineages, with connectivity patterns associated with worldwide, latitudinal "bands." These imply that connectivity is strongly influenced by global atmospheric circulation patterns, with dispersal and establishment beyond these latitudinal bands less common. Biogeographic patterns were less clear within the nuclear marker, with gene duplication likely hindering the detection of these. Divergence time analyses indicated that the current matrilineal population structure in C. purpureus has developed over the past six million years, with lineages diverging during the late Miocene, Pliocene, and Quaternary. Several colonization events in the Antarctic were apparent, as well as one old and distinct Antarctic clade, possibly isolated on the continent since the Pliocene. As C. purpureus is considered a model organism, the matrilineal biogeographic structure identified here provides a useful framework for future genetic and developmental studies on bryophytes. Our general findings may also be relevant to understanding global environmental influences on the biogeography of other organisms with microscopic propagules (e.g., spores) dispersed by wind.
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Affiliation(s)
- Elisabeth M. Biersma
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge, United Kingdom
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter Convey
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge, United Kingdom
| | - Rhys Wyber
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, NSW, Australia
| | - Sharon A. Robinson
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, NSW, Australia
| | - Mark Dowton
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Bart van de Vijver
- Research Department, Botanic Garden Meise, Meise, Belgium
- Ecosystem Management (ECOBE), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Katrin Linse
- Biodiversity, Evolution and Adaptation Team, British Antarctic Survey, Cambridge, United Kingdom
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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5
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Johannesson K, Zagrodzka Z, Faria R, Marie Westram A, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? J Evol Biol 2019; 33:342-351. [PMID: 31724256 PMCID: PMC7079066 DOI: 10.1111/jeb.13570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Zuzanna Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Rui Faria
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | | | - Roger K Butlin
- Department of Marine Sciences at Tjärnö, University of Gothenburg, Strömstad, Sweden.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
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6
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Nieto-Lugilde M, Werner O, McDaniel SF, Koutecký P, Kučera J, Rizk SM, Ros RM. Peripatric speciation associated with genome expansion and female-biased sex ratios in the moss genus Ceratodon. AMERICAN JOURNAL OF BOTANY 2018; 105:1009-1020. [PMID: 29957852 DOI: 10.1002/ajb2.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY A period of allopatry is widely believed to be essential for the evolution of reproductive isolation. However, strict allopatry may be difficult to achieve in some cosmopolitan, spore-dispersed groups, like mosses. We examined the genetic and genome size diversity in Mediterranean populations of the moss Ceratodon purpureus s.l. to evaluate the role of allopatry and ploidy change in population divergence. METHODS We sampled populations of the genus Ceratodon from mountainous areas and lowlands of the Mediterranean region, and from Western and Central Europe. We performed phylogenetic and coalescent analyses on sequences from five nuclear introns and a chloroplast locus to reconstruct their evolutionary history. We also estimated genome size using flow cytometry (employing propidium iodide) and determined the sex of samples using a sex-linked PCR marker. KEY RESULTS Two well-differentiated clades were resolved, discriminating two homogeneous groups: the widespread C. purpureus and a local group mostly restricted to the mountains in Southern Spain. The latter also possessed a genome size 25% larger than the widespread C. purpureus, and the samples of this group consist entirely of females. We also found hybrids, and some of them had a genome size equivalent to the sum of the C. purpureus and Spanish genome, suggesting that they arose by allopolyploidy. CONCLUSIONS These data suggest that a new species of Ceratodon arose via peripatric speciation, potentially involving a genome size change and a strong female-biased sex ratio. The new species has hybridized in the past with C. purpureus.
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Affiliation(s)
- Marta Nieto-Lugilde
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
| | - Olaf Werner
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
| | - Stuart F McDaniel
- Biology Department, University of Florida, Gainesville, Florida, 32611, USA
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
| | - Jan Kučera
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-370 05, České Budějovice, Czech Republic
| | - Samah Mohamed Rizk
- Genetics Department, Faculty of Agriculture, Ain Shams University, 68 Hadayek Shubra, 11241, Cairo, Egypt
| | - Rosa M Ros
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100, Murcia, Spain
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Baughman JT, Payton AC, Paasch AE, Fisher KM, McDaniel SF. Multiple factors influence population sex ratios in the Mojave Desert moss Syntrichia caninervis. AMERICAN JOURNAL OF BOTANY 2017; 104:733-742. [PMID: 28490519 DOI: 10.3732/ajb.1700045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF RESEARCH Natural populations of many mosses appear highly female-biased based on the presence of reproductive structures. This bias could be caused by increased male mortality, lower male growth rate, or a higher threshold for achieving sexual maturity in males. Here we test these hypotheses using samples from two populations of the Mojave Desert moss Syntrichia caninervis. METHODS We used double-digest restriction-site associated DNA (RAD) sequencing to identify candidate sex-associated loci in a panel of sex-expressing plants. Next, we used putative sex-associated markers to identify the sex of individuals without sex structures. KEY RESULTS We found a 17:1 patch-level phenotypic female to male sex ratio in the higher elevation site (Wrightwood) and no sex expression at the low elevation site (Phelan). In contrast, on the basis of genetic data, we found a 2:1 female bias at the Wrightwood site and only females at the Phelan site. The relative area occupied by male and female genets was indistinguishable, but males were less genetically diverse. CONCLUSIONS Our data suggest that both male-biased mortality and sexual dimorphism in thresholds for sex expression could explain genetic and phenotypic sex ratio biases and that phenotypic sex expression alone over-estimates the extent of actual sex ratio bias present in these two populations of S. caninervis.
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Affiliation(s)
- Jenna T Baughman
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Adam C Payton
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida 32611 USA
| | - Amber E Paasch
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Kirsten M Fisher
- Department of Biological Sciences, California State University, 5151 State University Drive, Los Angeles, California 90032 USA
| | - Stuart F McDaniel
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, Florida 32611 USA
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8
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Knegt B, Potter T, Pearson NA, Sato Y, Staudacher H, Schimmel BCJ, Kiers ET, Egas M. Detection of genetic incompatibilities in non-model systems using simple genetic markers: hybrid breakdown in the haplodiploid spider mite Tetranychus evansi. Heredity (Edinb) 2016; 118:311-321. [PMID: 27782117 PMCID: PMC5345600 DOI: 10.1038/hdy.2016.103] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 02/01/2023] Open
Abstract
When two related species interbreed, their hybrid offspring frequently suffer from reduced fitness. The genetics of hybrid incompatibility are described by the Bateson–Dobzhansky–Muller (BDM) model, where fitness is reduced by epistatic interactions between alleles of heterospecific origin. Unfortunately, most empirical evidence for the BDM model comes from a few well-studied model organisms, restricting our genetic understanding of hybrid incompatibilities to limited taxa. These systems are predominantly diploid and incompatibility is often complete, which complicates the detection of recessive allelic interactions and excludes the possibility to study viable or intermediate stages. Here, we advocate research into non-model organisms with haploid or haplodiploid reproductive systems and incomplete hybrid incompatibility because (1) dominance is absent in haploids and (2) incomplete incompatibility allows comparing affected with unaffected individuals. We describe a novel two-locus statistic specifying the frequency of individuals for which two alleles co-occur. This approach to studying BDM incompatibilities requires genotypic characterization of hybrid individuals, but not genetic mapping or genome sequencing. To illustrate our approach, we investigated genetic causes for hybrid incompatibility between differentiated lineages of the haplodiploid spider mite Tetranychus evansi, and show that strong, but incomplete, hybrid breakdown occurs. In addition, by comparing the genotypes of viable hybrid males and inviable hybrid male eggs for eight microsatellite loci, we show that nuclear and cytonuclear BDM interactions constitute the basis of hybrid incompatibility in this species. Our approach opens up possibilities to study BDM interactions in non-model taxa, and may give further insight into the genetic mechanisms behind hybrid incompatibility.
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Affiliation(s)
- B Knegt
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - T Potter
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - N A Pearson
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Y Sato
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.,Sugadaira Montane Research Center, University of Tsukuba, Ueda, Japan
| | - H Staudacher
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - B C J Schimmel
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - E T Kiers
- Department of Ecological Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - M Egas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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9
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Magdy M, Werner O, McDaniel SF, Goffinet B, Ros RM. Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains, Spain. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:280-288. [PMID: 26284822 DOI: 10.1111/plb.12381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 08/11/2015] [Indexed: 06/04/2023]
Abstract
The common cord moss Funaria hygrometrica has a worldwide distribution and thrives in a wide variety of environments. Here, we studied the genetic diversity in F. hygrometrica along an abiotic gradient in the Mediterranean high mountain of Sierra Nevada (Spain) using a genome scan method. Eighty-four samples from 17 locations from 24 to 2700 m were fingerprinted based on their amplified fragment length polymorphism (AFLP) banding pattern. Using PCA and Bayesian inference we found that the genetic diversity was structured in three or four clusters, respectively. Using a genome scan method we identified 13 outlier loci, which showed a signature of positive selection. Partial Mantel tests were performed between the Euclidean distance matrices of geographic and climatic variables, versus the pair-wise genetic distance of the AFLP dataset and AFLP-positive outliers dataset. AFLP-positive outlier data were significantly correlated with the gradient of the climatic variables, suggesting adaptive variation among populations of F. hygrometrica along the Sierra Nevada Mountains. We highlight the additional analyses necessary to identify the nature of these loci, and their biological role in the adaptation process.
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Affiliation(s)
- M Magdy
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - O Werner
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - S F McDaniel
- Biology Department, University of Florida, Gainesville, FL, USA
| | - B Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - R M Ros
- Departamento de Biología Vegetal, Facultad de Biología, Universidad de Murcia, Murcia, Spain
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Bisang I, Ehrlén J, Korpelainen H, Hedenäs L. No evidence of sexual niche partitioning in a dioecious moss with rare sexual reproduction. ANNALS OF BOTANY 2015; 116:771-9. [PMID: 26359424 PMCID: PMC4590334 DOI: 10.1093/aob/mcv133] [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: 04/04/2015] [Revised: 05/08/2015] [Accepted: 07/20/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND AIMS Roughly half of the species of bryophytes have separate sexes (dioecious) and half are hermaphroditic (monoecious). This variation has major consequences for the ecology and evolution of the different species. In some sexually reproducing dioecious bryophytes, sex ratio has been shown to vary with environmental conditions. This study focuses on the dioecious wetland moss Drepanocladus trifarius, which rarely produces sexual branches or sporophytes and lacks apparent secondary sex characteristics, and examines whether genetic sexes exhibit different habitat preferences, i.e. whether sexual niche partitioning occurs. METHODS A total of 277 shoots of D. trifarius were randomly sampled at 214 locations and 12 environmental factors were quantified at each site. Sex was assigned to the individual shoots collected in the natural environments, regardless of their reproductive status, using a specifically designed molecular marker associated with female sex. KEY RESULTS Male and female shoots did not differ in shoot biomass, the sexes were randomly distributed with respect to each other, and environmental conditions at male and female sampling locations did not differ. Collectively, this demonstrates a lack of sexual niche segregation. Adult genetic sex ratio was female-biased, with 2·8 females for every male individual. CONCLUSIONS The results show that although the sexes of D. trifarius did not differ with regard to annual growth, spatial distribution or habitat requirements, the genetic sex ratio was nevertheless significantly female-biased. This supports the notion that factors other than sex-related differences in reproductive costs and sexual dimorphism can also drive the evolution of biased sex ratios in plants.
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Affiliation(s)
- Irene Bisang
- Swedish Museum of Natural History, Department of Botany, Box 50007, SE-104 05 Stockholm, Sweden,
| | - Johan Ehrlén
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden and
| | - Helena Korpelainen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014 Helsinki, Finland
| | - Lars Hedenäs
- Swedish Museum of Natural History, Department of Botany, Box 50007, SE-104 05 Stockholm, Sweden
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Baack E, Melo MC, Rieseberg LH, Ortiz-Barrientos D. The origins of reproductive isolation in plants. THE NEW PHYTOLOGIST 2015; 207:968-84. [PMID: 25944305 DOI: 10.1111/nph.13424] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/16/2015] [Indexed: 05/23/2023]
Abstract
Reproductive isolation in plants occurs through multiple barriers that restrict gene flow between populations, but their origins remain uncertain. Work in the past decade has shown that postpollination barriers, such as the failure to form hybrid seeds or sterility of hybrid offspring, are often less strong than prepollination barriers. Evidence implicates multiple evolutionary forces in the origins of reproductive barriers, including mutation, stochastic processes and natural selection. Although adaptation to different environments is a common element of reproductive isolation, genomic conflicts also play a role, including female meiotic drive. The genetic basis of some reproductive barriers, particularly flower colour influencing pollinator behaviour, is well understood in some species, but the genetic changes underlying many other barriers, especially pollen-stylar interactions, are largely unknown. Postpollination barriers appear to accumulate at a faster rate in annuals compared with perennials, due in part to chromosomal rearrangements. Chromosomal changes can be important isolating barriers in themselves but may also reduce the recombination of genes contributing to isolation. Important questions for the next decade include identifying the evolutionary forces responsible for chromosomal rearrangements, determining how often prezygotic barriers arise due to selection against hybrids, and establishing the relative importance of genomic conflicts in speciation.
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Affiliation(s)
- Eric Baack
- Department of Biology, Luther College, Decorah, IA, 52101, USA
| | - Maria Clara Melo
- School of Biological Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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Johnson MG, Shaw AJ. Genetic diversity, sexual condition, and microhabitat preference determine mating patterns inSphagnum(Sphagnaceae) peat-mosses. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12497] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Matthew G. Johnson
- Biology Department; Duke University; 130 Science Drive Box 90338 Durham NC 27708 USA
| | - A. Jonathan Shaw
- Biology Department; Duke University; 130 Science Drive Box 90338 Durham NC 27708 USA
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Matsubara K, Yamamoto E, Mizobuchi R, Yonemaru JI, Yamamoto T, Kato H, Yano M. Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.). J Hered 2014; 106:113-22. [PMID: 25429024 DOI: 10.1093/jhered/esu065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F1s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.
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Affiliation(s)
- Kazuki Matsubara
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Eiji Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Ritsuko Mizobuchi
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Jun-ichi Yonemaru
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Toshio Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Hiroshi Kato
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Masahiro Yano
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
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McDaniel SF, Neubig KM, Payton AC, Quatrano RS, Cove DJ. Recent gene-capture on the UV sex chromosomes of the moss Ceratodon purpureus. Evolution 2013; 67:2811-22. [PMID: 24094335 DOI: 10.1111/evo.12165] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 05/02/2013] [Indexed: 01/12/2023]
Abstract
Sex chromosomes evolve from ordinary autosomes through the expansion and subsequent degeneration of a region of suppressed recombination that is inherited through one sex. Here we investigate the relative timing of these processes in the UV sex chromosomes of the moss Ceratodon purpureus using molecular population genetic analyses of eight newly discovered sex-linked loci. In this system, recombination is suppressed on both the female-transmitted (U) sex chromosome and the male-transmitted (V) chromosome. Genes on both chromosomes therefore should show the deleterious effects of suppressed recombination and sex-limited transmission, while purifying selection should maintain homologs of genes essential for both sexes on both sex chromosomes. Based on analyses of eight sex-linked loci, we show that the nonrecombining portions of the U and V chromosomes expanded in at least two events (~0.6-1.3 MYA and ~2.8-3.5 MYA), after the divergence of C. purpureus from its dioecious sister species, Trichodon cylindricus and Cheilothela chloropus. Both U- and V-linked copies showed reduced nucleotide diversity and limited population structure, compared to autosomal loci, suggesting that the sex chromosomes experienced more recent selective sweeps that the autosomes. Collectively these results highlight the dynamic nature of gene composition and molecular evolution on nonrecombining portions of the U and V sex chromosomes.
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Affiliation(s)
- Stuart F McDaniel
- Biology Department, University of Florida, Gainesville, Florida, 32611.
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Investigating incipient speciation in Arabidopsis lyrata from patterns of transmission ratio distortion. Genetics 2013; 194:697-708. [PMID: 23666938 DOI: 10.1534/genetics.113.152561] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F2 progenies of three reciprocal crosses between four natural populations. We found that the degree of TRD increases with genetic distance between crossed populations, but also that reciprocal progenies may differ substantially in their degree of TRD. Chromosomes AL6 and especially AL1 appear to be involved in many single- and two-locus distortions, but the location and source of TRD vary between crosses and between reciprocal progenies. We also found that the majority of single- and two-locus TRD appears to have a gametic, as opposed to zygotic, origin. Thus, while theory on BDM incompatibilities is typically illustrated with derived nuclear alleles proving incompatible in hybrid zygotes, our results suggest a prominent role for distortions emerging before zygote formation.
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McDaniel SF, van Baren MJ, Jones KS, Payton AC, Quatrano RS. Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon-primed, intron-spanning nuclear loci. APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1200387. [PMID: 25202534 PMCID: PMC4105291 DOI: 10.3732/apps.1200387] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/08/2012] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY We developed and tested primers for 218 nuclear loci for studying population genetics, phylogeography, and genome evolution in bryophytes. • METHODS AND RESULTS We aligned expressed sequence tags (ESTs) from Ceratodon purpureus to the Physcomitrella patens genome sequence, and designed primers that are homologous to conserved exons but span introns in the P. patens genome. We tested these primers on four isolates from New York, USA; Otavalo, Ecuador; and two laboratory isolates from Austria (WT4 and GG1). The median genome-wide nucleotide diversity was 0.008 substitutions/site, but the range was large (0-0.14), illustrating the among-locus heterogeneity in the species. • CONCLUSIONS These loci provide a valuable resource for finely resolved, genome-wide population genetic and species-level phylogenetic analyses of C. purpureus and its relatives.
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Affiliation(s)
- Stuart F. McDaniel
- Biology Department, University of Florida, Gainesville, Florida 32611 USA
- Biology Department, Washington University in St. Louis, St. Louis, Missouri 63130 USA
| | - Marijke J. van Baren
- Center for Genome Sciences, Washington University in St. Louis, St. Louis, Missouri 63130 USA
| | - Kelly S. Jones
- Biology Department, University of Florida, Gainesville, Florida 32611 USA
| | - Adam C. Payton
- Biology Department, University of Florida, Gainesville, Florida 32611 USA
| | - Ralph S. Quatrano
- Biology Department, Washington University in St. Louis, St. Louis, Missouri 63130 USA
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Smith LM, Bomblies K, Weigel D. Complex evolutionary events at a tandem cluster of Arabidopsis thaliana genes resulting in a single-locus genetic incompatibility. PLoS Genet 2011; 7:e1002164. [PMID: 21779175 PMCID: PMC3136440 DOI: 10.1371/journal.pgen.1002164] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 05/17/2011] [Indexed: 12/31/2022] Open
Abstract
Non-additive interactions between genomes have important implications, not only for practical applications such as breeding, but also for understanding evolution. In extreme cases, genes from different genomic backgrounds may be incompatible and compromise normal development or physiology. Of particular interest are non-additive interactions of alleles at the same locus. For example, overdominant behavior of alleles, with respect to plant fitness, has been proposed as an important component of hybrid vigor, while underdominance may lead to reproductive isolation. Despite their importance, only a few cases of genetic over- or underdominance affecting plant growth or fitness are understood at the level of individual genes. Moreover, the relationship between biochemical and fitness effects may be complex: genetic overdominance, that is, increased or novel activity of a gene may lead to evolutionary underdominance expressed as hybrid weakness. Here, we describe a non-additive interaction between alleles at the Arabidopsis thaliana OAK (OUTGROWTH-ASSOCIATED PROTEIN KINASE) gene. OAK alleles from two different accessions interact in F1 hybrids to cause a variety of aberrant growth phenotypes that depend on a recently acquired promoter with a novel expression pattern. The OAK gene, which is located in a highly variable tandem array encoding closely related receptor-like kinases, is found in one third of A. thaliana accessions, but not in the reference accession Col-0. Besides recruitment of exons from nearby genes as promoter sequences, key events in OAK evolution include gene duplication and divergence of a potential ligand-binding domain. OAK kinase activity is required for the aberrant phenotypes, indicating it is not recognition of an aberrant protein, but rather a true gain of function, or overdominance for gene activity, that leads to this underdominance for fitness. Our work provides insights into how tandem arrays, which are particularly prone to frequent, complex rearrangements, can produce genetic novelty. While intraspecific hybrids are vitally important in modern agriculture because they often perform better than their inbred parents, certain hybrid combinations fail to develop normally and are inferior to their parents. We have identified an Arabidopsis thaliana hybrid with several aberrant growth phenotypes that are caused by divergence at a single locus encoding the receptor-like kinase OUTGROWTH-ASSOCIATED PROTEIN KINASE (OAK). OAK belongs to a group of similar genes arranged in a tandem cluster that varies substantially between A. thaliana strains. OAK originated through duplication within the cluster with concurrent recruitment of coding sequences from nearby genes to form a new promoter with a novel expression pattern. Kinase activity of OAK is required for its effects, indicating that it is not recognition of an aberrant protein but rather a true gain of function that leads to the incompatibility. Most of the incompatibility seems to come from divergence within the extracellular ligand-binding domain of the OAK protein, indicating that heterodimers of OAK may have higher affinity for a natural substrate compared to either homodimer. Finally, mis-expression of the incompatible OAK alleles from the promoter present in the reference strain of A. thaliana also leads to genetic incompatibility, but with different phenotypic outcomes.
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Affiliation(s)
- Lisa M. Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kirsten Bomblies
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- * E-mail:
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Perroud PF, Cove DJ, Quatrano RS, McDaniel SF. An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines. THE NEW PHYTOLOGIST 2011; 191:301-306. [PMID: 21366596 PMCID: PMC3445409 DOI: 10.1111/j.1469-8137.2011.03668.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• The sequencing of the Physcomitrella patens genome, combined with the high frequency of gene targeting in this species, makes it ideal for reverse genetic studies. For forward genetic studies, experimental crosses and genetic analysis of progeny are essential. • Since P. patens is monoicous, producing both male and female gametes on the same gametophore, and undergoing self-fertilization at a high frequency, the identification of crossed sporophytes is difficult. Usually spores from many sporophytes from a mixed culture must be tested for the production of recombinant progeny. • Here, we describe the use of transgenic lines that express a fluorescent transgene constitutively, to provide a direct visual screen for hybrid sporophytes. • We show that segregations in crosses obtained with this technique are as expected, and demonstrate its utility for the study of the rate of outcrossing between three isolates of P. patens.
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Affiliation(s)
- Pierre-François Perroud
- Department of Biology, Campus Box 1137, Washington University in St Louis, St Louis, MO 63130, USA
| | - David J. Cove
- Department of Biology, Campus Box 1137, Washington University in St Louis, St Louis, MO 63130, USA
- Centre for Plant Sciences, Leeds University, Leeds, LS2 9JT, UK
| | - Ralph S. Quatrano
- Department of Biology, Campus Box 1137, Washington University in St Louis, St Louis, MO 63130, USA
| | - Stuart F. McDaniel
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA
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Leppälä J, Savolainen O. Nuclear-cytoplasmic interactions reduce male fertility in hybrids of Arabidopsis lyrata subspecies. Evolution 2011; 65:2959-72. [PMID: 21967435 DOI: 10.1111/j.1558-5646.2011.01361.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examined the level of postzygotic reproductive isolation in F(1) and F(2) hybrids of reciprocal crosses between the Arabidopsis lyrata subspecies lyrata (North American) and petraea (European). Our main results are: first, the percentage of fertile pollen was significantly reduced in the F(1) and F(2) compared to the parental populations. Second, mean pollen fertility differed markedly between reciprocal crosses: 84% in the F(2) with ssp. lyrata cytoplasm and 61% in the F(2) with ssp. petraea cytoplasm. Third, 17% of the F(2) with ssp. petraea cytoplasm showed male sterility (produced less than 30 pollen grains in our subsample). The hybrids were female fertile. We used QTL mapping to find the genomic regions that determine pollen fertility and that restore cytoplasmic male sterility (CMS). In the F(2) with ssp. lyrata cytoplasm, an epistatic pair of QTLs was detected. In the reciprocal F(2) progeny, four QTLs demonstrated within-population polymorphism for hybrid male sterility. In addition, in the F(2) with ssp. petraea cytoplasm, there was a strong male fertility restorer locus on chromosome 2 where a cluster of CMS restorer gene-related PPR genes have been found in A. lyrata. Our results underline the importance of cytonuclear interactions in understanding genetics of the early stages of speciation.
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Affiliation(s)
- Johanna Leppälä
- Department of Biology and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland.
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Pritchard VL, Dimond L, Harrison JS, S Velázquez CC, Zieba JT, Burton RS, Edmands S. Interpopulation hybridization results in widespread viability selection across the genome in Tigriopus californicus. BMC Genet 2011; 12:54. [PMID: 21639918 PMCID: PMC3138442 DOI: 10.1186/1471-2156-12-54] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 06/03/2011] [Indexed: 11/10/2022] Open
Abstract
Background Genetic interactions within hybrids influence their overall fitness. Understanding the details of these interactions can improve our understanding of speciation. One experimental approach is to investigate deviations from Mendelian expectations (segregation distortion) in the inheritance of mapped genetic markers. In this study, we used the copepod Tigriopus californicus, a species which exhibits high genetic divergence between populations and a general pattern of reduced fitness in F2 interpopulation hybrids. Previous studies have implicated both nuclear-cytoplasmic and nuclear-nuclear interactions in causing this fitness reduction. We identified and mapped population-diagnostic single nucleotide polymorphisms (SNPs) and used these to examine segregation distortion across the genome within F2 hybrids. Results We generated a linkage map which included 45 newly elucidated SNPs and 8 population-diagnostic microsatellites used in previous studies. The map, the first available for the Copepoda, was estimated to cover 75% of the genome and included markers on all 12 T. californicus chromosomes. We observed little segregation distortion in newly hatched F2 hybrid larvae (fewer than 10% of markers at p < 0.05), but strikingly higher distortion in F2 hybrid adult males (45% of markers at p < 0.05). Hence, segregation distortion was primarily caused by selection against particular genetic combinations which acted between hatching and maturity. Distorted markers were not distributed randomly across the genome but clustered on particular chromosomes. In contrast to other studies in this species we found little evidence for cytonuclear coadaptation. Instead, different linkage groups exhibited markedly different patterns of distortion, which appear to have been influenced by nuclear-nuclear epistatic interactions and may also reflect genetic load carried within the parental lines. Conclusion Adult male F2 hybrids between two populations of T. californius exhibit dramatic segregation distortion across the genome. Distorted loci are clustered within specific linkage groups, and the direction of distortion differs between chromosomes. This segregation distortion is due to selection acting between hatching and adulthood.
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Affiliation(s)
- Victoria L Pritchard
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, USA.
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Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS. The moss Physcomitrella patens: a novel model system for plant development and genomic studies. Cold Spring Harb Protoc 2010; 2009:pdb.emo115. [PMID: 20147063 DOI: 10.1101/pdb.emo115] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David J Cove
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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HEDENÄS LARS, BISANG IRENE, KORPELAINEN HELENA, CRONHOLM BODIL. The true sex ratio in European Pseudocalliergon trifarium (Bryophyta: Amblystegiaceae) revealed by a novel molecular approach. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01408.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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McDaniel SF, von Stackelberg M, Richardt S, Quatrano RS, Reski R, Rensing SA. THE SPECIATION HISTORY OF THEPHYSCOMITRIUM-PHYSCOMITRELLASPECIES COMPLEX. Evolution 2010; 64:217-31. [DOI: 10.1111/j.1558-5646.2009.00797.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kliebenstein D. Advancing genetic theory and application by metabolic quantitative trait loci analysis. THE PLANT CELL 2009; 21:1637-46. [PMID: 19525414 PMCID: PMC2714920 DOI: 10.1105/tpc.109.067611] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 05/12/2009] [Accepted: 06/04/2009] [Indexed: 05/18/2023]
Abstract
This review describes recent advances in the analysis of metabolism using quantitative genetics. It focuses on how recent metabolic quantitative trait loci (QTL) studies enhance our understanding of the genetic architecture underlying naturally variable phenotypes and the impact of this fundamental research on agriculture, specifically crop breeding. In particular, the role of whole-genome duplications in generating quantitative genetic variation within a species is highlighted and the potential uses of this phenomenon presented. Additionally, the review describes how new observations from metabolic QTL mapping analyses are helping to shape and expand the concepts of genetic epistasis.
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Affiliation(s)
- Danielj Kliebenstein
- Genetics Graduate Group and Department of Plant Sciences, University of California, Davis, California 95616, USA.
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