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Li LL, Xiao Y, Wang X, He ZH, Lv YW, Hu XS. The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection. Genome Biol Evol 2023; 15:evad151. [PMID: 37561000 PMCID: PMC10443736 DOI: 10.1093/gbe/evad151] [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: 01/11/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Alternation of generations in plant life cycle provides a biological basis for natural selection occurring in either the gametophyte or the sporophyte phase or in both. Divergent biphasic selection could yield distinct evolutionary rates for phase-specific or pleiotropic genes. Here, we analyze models that deal with antagonistic and synergistic selection between alternative generations in terms of the ratio of nonsynonymous to synonymous divergence (Ka/Ks). Effects of biphasic selection are opposite under antagonistic selection but cumulative under synergistic selection for pleiotropic genes. Under the additive and comparable strengths of biphasic allelic selection, the absolute Ka/Ks for the gametophyte gene is equal to in outcrossing but smaller than, in a mixed mating system, that for the sporophyte gene under antagonistic selection. The same pattern is predicted for Ka/Ks under synergistic selection. Selfing reduces efficacy of gametophytic selection. Other processes, including pollen and seed flow and genetic drift, reduce selection efficacy. The polymorphism (πa) at a nonsynonymous site is affected by the joint effects of selfing with gametophytic or sporophytic selection. Likewise, the ratio of nonsynonymous to synonymous polymorphism (πa/πs) is also affected by the same joint effects. Gene flow and genetic drift have opposite effects on πa or πa/πs in interacting with gametophytic and sporophytic selection. We discuss implications of this theory for detecting natural selection in terms of Ka/Ks and for interpreting the evolutionary divergence among gametophyte-specific, sporophyte-specific, and pleiotropic genes.
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Affiliation(s)
- Ling-Ling Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
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Duan Y, Yan J, Zhu Y, Zhang C, Tao X, Ji H, Zhang M, Wang X, Wang L. Limited accumulation of high-frequency somatic mutations in a 1700-year-old Osmanthus fragrans tree. TREE PHYSIOLOGY 2022; 42:2040-2049. [PMID: 35640149 DOI: 10.1093/treephys/tpac058] [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: 01/10/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]
Abstract
Lifespan varies greatly between and within species. Mutation accumulation is considered an important factor explaining this life-history trait. However, direct assessment of somatic mutations in long-lived species is still rare. In this study, we sequenced a 1700-year-old sweet olive tree and analysed the high-frequency somatic mutations accumulated in its six primary branches. We found the lowest per-year mutation accumulation rate in this oldest tree among those studied via the whole-genome sequencing approach. Investigation of mutation profiles suggests that this low rate of high-frequency mutation was unlikely to result from strong purifying selection. More intriguingly, on a per-branching scale, the high-frequency mutation accumulation rate was similar among the long-lived individuals such as oak, wild peach and sweet olive investigated here. We therefore suggest the possibility that the accumulation of high-frequency somatic mutations in very long-lived trees might have an upper boundary due to both the possible limited number of stem cell divisions and the early segregation of the stem cell lineage.
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Affiliation(s)
- Yifan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
| | - Jiping Yan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
| | - Yue Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
| | - Cheng Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
| | - Xiuhua Tao
- Vegetable and Flowers Research Institute, Jiangxi Academy of Agricultural Sciences, 1738 Liantang Middle Blvd, Nanchang 330200, China
| | - Hongli Ji
- Vegetable and Flowers Research Institute, Jiangxi Academy of Agricultural Sciences, 1738 Liantang Middle Blvd, Nanchang 330200, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
| | - Xianrong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
- International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, 159 Longpan Road, Xuanwu District, Nanjing 210037, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Qixia District. Nanjing 210023, China
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3
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Jaron KS, Bast J, Nowell RW, Ranallo-Benavidez TR, Robinson-Rechavi M, Schwander T. Genomic Features of Parthenogenetic Animals. J Hered 2021; 112:19-33. [PMID: 32985658 PMCID: PMC7953838 DOI: 10.1093/jhered/esaa031] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Evolution without sex is predicted to impact genomes in numerous ways. Case studies of individual parthenogenetic animals have reported peculiar genomic features that were suggested to be caused by their mode of reproduction, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 parthenogenetic animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature was systematically replicated across a majority of these transitions, suggesting that previously reported patterns were lineage-specific rather than illustrating the general consequences of parthenogenesis. We found that only parthenogens of hybrid origin were characterized by high heterozygosity levels. Parthenogens that were not of hybrid origin appeared to be largely homozygous, independent of the cellular mechanism underlying parthenogenesis. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, the impact of the origin of parthenogenesis, and a survivorship bias of parthenogenetic lineages.
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Affiliation(s)
- Kamil S Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
- Reuben W. Nowell is now at the Department of Zoology, University of Oxford, Oxford, UK
| | | | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Deleterious Mutation Burden and Its Association with Complex Traits in Sorghum ( Sorghum bicolor). Genetics 2019; 211:1075-1087. [PMID: 30622134 PMCID: PMC6404259 DOI: 10.1534/genetics.118.301742] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/22/2018] [Indexed: 11/18/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a major staple food cereal for millions of people worldwide. Valluru et al. identify putative deleterious mutations among ∼5.5M segregating variants of 229 diverse sorghum... Sorghum (Sorghum bicolor L.) is a major food cereal for millions of people worldwide. The sorghum genome, like other species, accumulates deleterious mutations, likely impacting its fitness. The lack of recombination, drift, and the coupling with favorable loci impede the removal of deleterious mutations from the genome by selection. To study how deleterious variants impact phenotypes, we identified putative deleterious mutations among ∼5.5 M segregating variants of 229 diverse biomass sorghum lines. We provide the whole-genome estimate of the deleterious burden in sorghum, showing that ∼33% of nonsynonymous substitutions are putatively deleterious. The pattern of mutation burden varies appreciably among racial groups. Across racial groups, the mutation burden correlated negatively with biomass, plant height, specific leaf area (SLA), and tissue starch content (TSC), suggesting that deleterious burden decreases trait fitness. Putatively deleterious variants explain roughly one-half of the genetic variance. However, there is only moderate improvement in total heritable variance explained for biomass (7.6%) and plant height (average of 3.1% across all stages). There is no advantage in total heritable variance for SLA and TSC. The contribution of putatively deleterious variants to phenotypic diversity therefore appears to be dependent on the genetic architecture of traits. Overall, these results suggest that incorporating putatively deleterious variants into genomic models slightly improves prediction accuracy because of extensive linkage. Knowledge of deleterious variants could be leveraged for sorghum breeding through either genome editing and/or conventional breeding that focuses on the selection of progeny with fewer deleterious alleles.
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Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
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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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Darolti I, Wright AE, Pucholt P, Berlin S, Mank JE. Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis. Mol Ecol 2018; 27:694-708. [PMID: 29274186 PMCID: PMC5901004 DOI: 10.1111/mec.14466] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 12/13/2022]
Abstract
The relative rate of evolution for sex‐biased genes has often been used as a measure of the strength of sex‐specific selection. In contrast to studies in a wide variety of animals, far less is known about the molecular evolution of sex‐biased genes in plants, particularly in dioecious angiosperms. Here, we investigate the gene expression patterns and evolution of sex‐biased genes in the dioecious plant Salix viminalis. We observe lower rates of sequence evolution for male‐biased genes expressed in the reproductive tissue compared to unbiased and female‐biased genes. These results could be partially explained by the lower codon usage bias for male‐biased genes leading to elevated rates of synonymous substitutions compared to unbiased genes. However, the stronger haploid selection in the reproductive tissue of plants, together with pollen competition, would also lead to higher levels of purifying selection acting to remove deleterious variation. Future work should focus on the differential evolution of haploid‐ and diploid‐specific genes to understand the selective dynamics acting on these loci.
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Affiliation(s)
- Iulia Darolti
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Alison E Wright
- Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Pascal Pucholt
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Array and Analysis Facility, Department of Medical Science, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution and Environment, University College London, London, UK.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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Meleshko O, Stenøien HK, Speed JDM, Flatberg KI, Kyrkjeeide MO, Hassel K. Is interspecific gene flow and speciation in peatmosses ( Sphagnum) constrained by phylogenetic relationship and life-history traits? LINDBERGIA 2018. [DOI: 10.25227/linbg.01107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Olena Meleshko
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Hans K. Stenøien
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - James D. M. Speed
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Kjell I. Flatberg
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | | | - Kristian Hassel
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
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Hiss M, Meyberg R, Westermann J, Haas FB, Schneider L, Schallenberg-Rüdinger M, Ullrich KK, Rensing SA. Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens: introducing the ecotype Reute. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:606-620. [PMID: 28161906 DOI: 10.1111/tpj.13501] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 05/21/2023]
Abstract
Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences, and to investigate the effects of environmental adaption and acclimation. For the model moss Physcomitrella patens collections of accessions are available, and have been used for phylogenetic and taxonomic studies, for example, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing. We analysed cross-technology and cross-laboratory data to define a confident set of 15 mature sporophyte-specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes than Reute or Villersexel, although gametangia develop with the same time course and do not show evident morphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet we found variation between Gransden and Reute in the expression profiles of several genes, as well as variation hot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression differences between the ecotypes for selected candidate genes in the GRAS transcription factor family, the chalcone synthase family and in genes involved in cell wall modification that are potentially related to phenotypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse-genetics studies that involve progression through the life cycle and multiple generations.
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Affiliation(s)
- Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Jens Westermann
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Lucas Schneider
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | | | - Kristian K Ullrich
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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Morgan K, McGaughran A, Rödelsperger C, Sommer RJ. Variation in rates of spontaneous male production within the nematode species Pristionchus pacificus supports an adaptive role for males and outcrossing. BMC Evol Biol 2017; 17:57. [PMID: 28228092 PMCID: PMC5322664 DOI: 10.1186/s12862-017-0873-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 01/05/2017] [Indexed: 12/18/2022] Open
Abstract
Background The nematode species Pristionchus pacificus has an androdioecious mating system in which populations consist of self-fertilizing hermaphrodites and relatively few males. The prevalence of males in such a system is likely to depend on the relative pros and cons of outcrossing. While outcrossing generates novel allelic combinations and can therefore increase adaptive potential, it may also disrupt the potentially beneficial consequences of repeated generations of selfing. These include purging of deleterious alleles, inheritance of co-adapted allele complexes, improved hermaphrodite fitness and increased population growth. Here we use experimental and population genetic approaches to test hypotheses relating to male production and outcrossing in laboratory and natural populations of P. pacificus sampled from the volcanic island of La Réunion. Results We find a significant interaction between sampling locality and temperature treatment influencing rates of spontaneous male production in the laboratory. While strains isolated at higher altitude, cooler localities produce a higher proportion of male offspring at 25 °C relative to 20 or 15 °C, the reverse pattern is seen in strains isolated from warmer, low altitude localities. Linkage disequilibrium extends across long physical distances, but fails to approach levels reported for the partially selfing nematode species Caenorhabditis elegans. Finally, we find evidence for admixture between divergent genetic lineages. Conclusions Elevated rates of laboratory male generation appear to occur under environmental conditions which differ from those experienced by populations in nature. Such elevated male generation may result in higher outcrossing rates, hence driving increased effective recombination and the creation of potentially adaptive novel allelic combinations. Patterns of linkage disequilibrium decay support selfing as the predominant reproductive strategy in P. pacificus. Finally, despite the potential for outcrossing depression, our results suggest admixture has occurred between distinct genetic lineages since their independent colonization of the island, suggesting outcrossing depression may not be uniform in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0873-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katy Morgan
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany. .,Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA70148, USA.
| | - Angela McGaughran
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,CSIRO Land & Water, Black Mountain Laboratories, Clunies Ross Street, Canberra, ACT 2601, Australia.,University of Melbourne, School of BioSciences, 30 Flemington Road, Melbourne, VIC, 3010, Australia
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
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11
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Broz AK, Randle AM, Sianta SA, Tovar-Méndez A, McClure B, Bedinger PA. Mating system transitions in Solanum habrochaites impact interactions between populations and species. THE NEW PHYTOLOGIST 2017; 213:440-454. [PMID: 27516156 DOI: 10.1111/nph.14130] [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: 05/02/2016] [Accepted: 07/01/2016] [Indexed: 05/23/2023]
Abstract
In plants, transitions in mating system from outcrossing to self-fertilization are common; however, the impact of these transitions on interspecific and interpopulation reproductive barriers is not fully understood. We examined the consequences of mating system transition for reproductive barriers in 19 populations of the wild tomato species Solanum habrochaites. We identified S. habrochaites populations with self-incompatible (SI), self-compatible (SC) and mixed population (MP) mating systems, and characterized pollen-pistil interactions among S. habrochaites populations and between S. habrochaites and other tomato species. We examined the relationship between mating system, floral morphology, interspecific and interpopulation compatibility and pistil SI factors. We documented five distinct phenotypic groups by combining reproductive behavior with molecular data. Transitions from SI to MP were not associated with weakened interspecific reproductive barriers or loss of known pistil SI factors. However, transitions to SC at the northern range margin were accompanied by loss of S-RNase, smaller flowers, and weakened (or absent) interspecific pollen-pistil barriers. Finally, we identified a subset of SC populations that exhibited a partial interpopulation reproductive barrier with central SI populations. Our results support the hypothesis that shifts in mating system, followed by additional loss-of-function mutations, impact reproductive barriers within and between species.
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Affiliation(s)
- Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - April M Randle
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
- Department of Environmental Science, University of San Francisco, San Francisco, CA, 94117, USA
| | - Shelley A Sianta
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | | | - Bruce McClure
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Patricia A Bedinger
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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12
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Rousselle M, Faivre N, Ballenghien M, Galtier N, Nabholz B. Hemizygosity Enhances Purifying Selection: Lack of Fast-Z Evolution in Two Satyrine Butterflies. Genome Biol Evol 2016; 8:3108-3119. [PMID: 27590089 PMCID: PMC5174731 DOI: 10.1093/gbe/evw214] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The fixation probability of a recessive beneficial mutation is increased on the X or Z chromosome, relative to autosomes, because recessive alleles carried by X or Z are exposed to selection in the heterogametic sex. This leads to an increased dN/dS ratio on sex chromosomes relative to autosomes, a pattern called the “fast-X” or “fast-Z” effect. Besides positive selection, the strength of genetic drift and the efficacy of purifying selection, which affect the rate of molecular evolution, might differ between sex chromosomes and autosomes. Disentangling the complex effects of these distinct forces requires the genome-wide analysis of polymorphism, divergence and gene expression data in a variety of taxa. Here we study the influence of hemizygosity of the Z chromosome in Maniola jurtina and Pyronia tithonus, two species of butterflies (Lepidoptera, Nymphalidae, Satyrinae). Using transcriptome data, we compare the strength of positive and negative selection between Z and autosomes accounting for sex-specific gene expression. We show that M. jurtina and P. tithonus do not experience a faster, but rather a slightly slower evolutionary rate on the Z than on autosomes. Our analysis failed to detect a significant difference in adaptive evolutionary rate between Z and autosomes, but comparison of male-biased, unbiased and female-biased Z-linked genes revealed an increased efficacy of purifying selection against recessive deleterious mutations in female-biased Z-linked genes. This probably contributes to the lack of fast-Z evolution of satyrines. We suggest that the effect of hemizygosity on the fate of recessive deleterious mutations should be taken into account when interpreting patterns of molecular evolution in sex chromosomes vs. autosomes.
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Affiliation(s)
- Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Faivre
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Marion Ballenghien
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Nicolas Galtier
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
| | - Benoit Nabholz
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Place E. Bataillon, Montpellier, France
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13
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Krueger‐Hadfield SA, Kollars NM, Byers JE, Greig TW, Hammann M, Murray DC, Murren CJ, Strand AE, Terada R, Weinberger F, Sotka EE. Invasion of novel habitats uncouples haplo‐diplontic life cycles. Mol Ecol 2016; 25:3801-16. [DOI: 10.1111/mec.13718] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/23/2016] [Accepted: 05/20/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Stacy A. Krueger‐Hadfield
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - Nicole M. Kollars
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - James E. Byers
- Odum School of Ecology University of Georgia 130 E. Green St. Athens GA 30602 USA
| | - Thomas W. Greig
- NOAA/National Ocean Service Center for Coastal Environmental Health and Biomolecular Research 219 Fort Johnson Rd Charleston SC 29312 USA
| | - Mareike Hammann
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 20 D‐23105 Kiel Germany
| | - David C. Murray
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
| | - Courtney J. Murren
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - Allan E. Strand
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
| | - Ryuta Terada
- Department of Fisheries Kagoshima University Shimoarata 3‐50‐20 Kagoshima City 890‐0056 Japan
| | - Florian Weinberger
- GEOMAR Helmholtz‐Zentrum für Ozeanforschung Kiel Düsternbrooker Weg 20 D‐23105 Kiel Germany
| | - Erik E. Sotka
- Grice Marine Laboratory College of Charleston 205 Fort Johnson Rd Charleston SC 29412 USA
- Department of Biology College of Charleston 66 George St. Charleston SC 29424 USA
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14
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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15
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Gossmann TI, Saleh D, Schmid MW, Spence MA, Schmid KJ. Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes. Mol Biol Evol 2016; 33:1669-78. [PMID: 26956888 PMCID: PMC4915351 DOI: 10.1093/molbev/msw044] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as "evolutionary bulge" during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants.
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Affiliation(s)
- Toni I Gossmann
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Dounia Saleh
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Marc W Schmid
- Institute for Plant Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Michael A Spence
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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16
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Parrish RC, Penley MJ, Morran LT. The Integral Role of Genetic Variation in the Evolution of Outcrossing in the Caenorhabditis elegans-Serratia marcescens Host-Parasite System. PLoS One 2016; 11:e0154463. [PMID: 27119159 PMCID: PMC4847799 DOI: 10.1371/journal.pone.0154463] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/13/2016] [Indexed: 12/05/2022] Open
Abstract
Outcrossing is predicted to facilitate more rapid adaptation than self-fertilization as a result of genetic exchange between genetically variable individuals. Such genetic exchange may increase the efficacy of selection by breaking down Hill-Robertson interference, as well as promoting the maintenance of within-lineage genetic diversity. Experimental studies have demonstrated the selective advantage of outcrossing in novel environments. Here, we assess the specific role of genetic variation in the evolution of outcrossing. We experimentally evolved genetically variable and inbred populations of mixed mating (outcrossing and self-fertilizing) Caenorhabditis elegans nematodes under novel ecological conditions—specifically the presence of the virulent parasite Serratia marcescens. Outcrossing rates increased in genetically variable host populations evolved in the presence of the parasite, whereas parasite exposure in inbred populations resulted in reduced rates of host outcrossing. The host populations with genetic variation also exhibited increased fitness in the presence of the parasite over eight generations, whereas inbred populations did not. This increase in fitness was primarily the result of adaptation to the parasite, rather than recovery from initial inbreeding depression. Therefore, the benefits of outcrossing were only manifested in the presence of genetic variation, and outcrossing was favored over self-fertilization as a result. As predicted, the benefits of outcrossing under novel ecological conditions are a product of genetic exchange between genetically diverse lineages.
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Affiliation(s)
- Raymond C. Parrish
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - McKenna J. Penley
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Levi T. Morran
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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17
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Shimizu KK, Tsuchimatsu T. Evolution of Selfing: Recurrent Patterns in Molecular Adaptation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054249] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of selfing is characterized by a loss of self-incompatibility, the selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asymmetry. Prevalence of dominant self-compatible mutations is consistent with Haldane's sieve, which acts against recessive adaptive mutations. Time estimates based on genome-wide polymorphisms and self-incompatibility genes generally support the recent origin of selfing.
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Affiliation(s)
- Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Takashi Tsuchimatsu
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
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18
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Balance between inbreeding and outcrossing in a nannandrous species, the moss Homalothecium lutescens. Heredity (Edinb) 2015; 116:107-13. [PMID: 26328759 DOI: 10.1038/hdy.2015.79] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/03/2015] [Accepted: 07/09/2015] [Indexed: 11/09/2022] Open
Abstract
Epiphytic dwarf males on the females present a possible solution to the problem of short fertilization distances in mosses. However, leptokurtic spore dispersal makes dwarf males likely to be closely related to their host shoot, with an accompanying risk of inbreeding. The capacity of a female to harbour a high number of different dwarf males suggests that there may be mechanisms in place that counteract inbreeding, such as polyandry and post-fertilization selection. We have genotyped sporophytes, female host shoots and dwarf males in four populations of the moss Homalothecium lutescens. We found no evidence of selective sporophyte abortion based on level of heterozygosity. The occurrence of entirely homozygous sporophytes together with significantly positive inbreeding coefficients in three of the populations (mean FIS between 0.48 and 0.64) suggest frequent mother-son mating events. However, 23% of all sampled sporophytes had a higher level of heterozygosity compared with the mean expected heterozygosity at the population level. Polyandry was frequent, on average 59% of the sporophytes on a female shoot were sired by distinct fathers. In conclusion, sporadic fertilizations by dwarf males originating from nonhost female shoots appear to counteract strong inbreeding.
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19
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Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. Mol Ecol 2015; 24:3093-106. [PMID: 25930165 PMCID: PMC4480654 DOI: 10.1111/mec.13221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 04/21/2015] [Accepted: 04/28/2015] [Indexed: 02/06/2023]
Abstract
Rapidly evolving proteins can aid the identification of genes underlying phenotypic adaptation across taxa, but functional and structural elements of genes can also affect evolutionary rates. In plants, the ‘edges’ of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region. However, the extent to which these regions may be masking indicators of positive selection or account for the relationship between dN/dS and other genomic parameters is unclear. We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana. We also obtain lineage-specific dN/dS estimates, making use of the recently sequenced genome of Thellungiella parvula, the second closest sequenced relative after the sister species Arabidopsis lyrata. Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level. Furthermore, the removal of exon edges shifts dN/dS estimates upwards, increasing the proportion of genes potentially under adaptive selection. We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters.
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Affiliation(s)
- Stephen J Bush
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Paula X Kover
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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20
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Hu XS. Mating system as a barrier to gene flow. Evolution 2015; 69:1158-77. [PMID: 25873333 DOI: 10.1111/evo.12660] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 04/07/2015] [Indexed: 12/16/2022]
Abstract
Understanding mating system as one of reproductive isolating barriers remains important although this barrier is classified in a different sense from behavioral, ecological, and mechanical isolating barriers. Selfing enhances incipient speciation while outcrossing facilitates species integrity. Here, I study how mating system affects gene exchanges between genetically diverging species in a hybrid zone. Results show that a predominant selfing species has a greater barrier to selective gene flow than does a predominant outcrossing species. Barrier to neutral gene flow convexly changes with the selfing rate due to linkage disequilibrium, with a maximum at around intermediate selfing rate. Asymmetric transient or steady-state barriers to neutral gene flow occur between two sides of a hybrid zone when the neutral gene is affected by its linked selective gene whose alternative alleles are adaptive to heterogeneous habitats. Selfing interacts with both a physical barrier and a density-dependent ecological regulation (a logarithmic model) to strengthen the barriers to neutral and selective gene flow. This theory helps to interpret incipient speciation driven by selfing or to explain the asymmetric gene flow or unequal genomic mixtures between closely related species caused by their asymmetric mating systems in natural hybrid zones.
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Affiliation(s)
- Xin-Sheng Hu
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, United Kingdom.
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21
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Russell SD, Jones DS. The male germline of angiosperms: repertoire of an inconspicuous but important cell lineage. FRONTIERS IN PLANT SCIENCE 2015; 6:173. [PMID: 25852722 PMCID: PMC4367165 DOI: 10.3389/fpls.2015.00173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/03/2015] [Indexed: 05/03/2023]
Abstract
The male germline of flowering plants constitutes a specialized lineage of diminutive cells initiated by an asymmetric division of the initial microspore cell that sequesters the generative cell from the pollen vegetative cell. The generative cell subsequently divides to form the two male gametes (non-motile sperm cells) that fuse with the two female gametophyte target cells (egg and central cells) to form the zygote and endosperm. Although these male gametes can be as little as 1/800th of the volume of their female counterpart, they encode a highly distinctive and rich transcriptome, translate proteins, and display a novel suite of gamete-distinctive control elements that create a unique chromatin environment in the male lineage. Sperm-expressed transcripts also include a high proportion of transposable element-related sequences that may be targets of non-coding RNA including miRNA and silencing elements from peripheral cells. The number of sperm-encoded transcripts is somewhat fewer than the number present in the egg cell, but are remarkably distinct compared to other cell types according to principal component and other analyses. The molecular role of the male germ lineage cells is just beginning to be understood and appears more complex than originally anticipated.
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Affiliation(s)
- Scott D. Russell
- *Correspondence: Scott D. Russell, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, 770 Van Vleet Oval, OK 73019, USA
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22
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The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations. Genetics 2014; 199:817-29. [PMID: 25552275 DOI: 10.1534/genetics.114.172809] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The transition from outcrossing to selfing is predicted to reduce the genome-wide efficacy of selection because of the lower effective population size (Ne) that accompanies this change in mating system. However, strongly recessive deleterious mutations exposed in the homozygous backgrounds of selfers should be under strong purifying selection. Here, we examine estimates of the distribution of fitness effects (DFE) and changes in the magnitude of effective selection coefficients (Nes) acting on mutations during the transition from outcrossing to selfing. Using forward simulations, we investigated the ability of a DFE inference approach to detect the joint influence of mating system and the dominance of deleterious mutations on selection efficacy. We investigated predictions from our simulations in the annual plant Eichhornia paniculata, in which selfing has evolved from outcrossing on multiple occasions. We used range-wide sampling to generate population genomic datasets and identified nonsynonymous and synonymous polymorphisms segregating in outcrossing and selfing populations. We found that the transition to selfing was accompanied by a change in the DFE, with a larger fraction of effectively neutral sites (Nes < 1), a result consistent with the effects of reduced Ne in selfers. Moreover, an increased proportion of sites in selfers were under strong purifying selection (Nes > 100), and simulations suggest that this is due to the exposure of recessive deleterious mutations. We conclude that the transition to selfing has been accompanied by the genome-wide influences of reduced Ne and strong purifying selection against deleterious recessive mutations, an example of purging at the molecular level.
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