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Miao X, Yang W, Li D, Wang A, Li J, Deng X, He L, Niu J. Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance. BMC PLANT BIOLOGY 2024; 24:628. [PMID: 38961375 PMCID: PMC11220973 DOI: 10.1186/s12870-024-05333-9] [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: 01/27/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. RESULTS We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. CONCLUSION We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.
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Affiliation(s)
- Xiaorong Miao
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wenwen Yang
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Donghai Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Aiqin Wang
- College of Agriculture, Guangxi University, Nanning, 530004, China.
| | - Juanyun Li
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Xu Deng
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China
| | - Longfei He
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Junqi Niu
- College of Agriculture, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Agricultural Resources Chemistry and Biotechnology, Agricultural College, Yulin Normal University, Yulin, 537000, China.
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Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M. Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Nat Ecol Evol 2024; 8:777-790. [PMID: 38383850 PMCID: PMC11009112 DOI: 10.1038/s41559-024-02329-4] [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: 10/09/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Chromosomes are a central unit of genome organization. One-tenth of all described species on Earth are butterflies and moths, the Lepidoptera, which generally possess 31 chromosomes. However, some species display dramatic variation in chromosome number. Here we analyse 210 chromosomally complete lepidopteran genomes and show that the chromosomes of extant lepidopterans are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact through 250 million years of evolution and diversification. Against this stable background, eight lineages have undergone extensive reorganization either through numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions often involve small, repeat-rich Merian elements and the sex-linked element. Our results reveal the constraints on genome architecture in Lepidoptera and provide a deeper understanding of chromosomal rearrangements in eukaryotic genome evolution.
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Affiliation(s)
| | - Lewis Stevens
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK.
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3
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de Oliveira TD, de Freitas TR. Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia). Genet Mol Biol 2024; 46:e20230180. [PMID: 38315881 PMCID: PMC10842476 DOI: 10.1590/1678-4685-gmb-2023-0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
Contrary to predictions from classical hybrid sterility models of chromosomal speciation, some organisms display high rates of karyotype variation. Ctenomys are the current mammals with the greatest interspecific and intraspecific chromosomal variation. A large number of species have been studied cytogenetically. The diploid numbers of chromosomes range from 2n = 10 to 2n = 70. Here, we analyzed karyotype evolution in Ctenomys using comparative phylogenetic methods. We found a strong phylogenetic signal with chromosome number. This refutes the chromosomal megaevolution model, which proposes the independent accumulation of multiple chromosomal rearrangements in each closely related species. We found that Brownian motion (BM) described the observed characteristic changes more thoroughly than the Ornstein-Uhlenbeck and Early-Burst models. This suggests that the evolution of chromosome numbers occurs by a random walk along phylogenetic clades. However, our data indicate that the BM model alone does not fully characterize the chromosomal evolution of Ctenomys.
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Affiliation(s)
- Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Thales R.O. de Freitas
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
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Elliott TL, Muasya AM, Bureš P. Complex patterns of ploidy in a holocentric plant clade (Schoenus, Cyperaceae) in the Cape biodiversity hotspot. ANNALS OF BOTANY 2023; 131:143-156. [PMID: 35226733 PMCID: PMC9904348 DOI: 10.1093/aob/mcac027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/27/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS It is unclear how widespread polyploidy is throughout the largest holocentric plant family - the Cyperaceae. Because of the prevalence of chromosomal fusions and fissions, which affect chromosome number but not genome size, it can be impossible to distinguish if individual plants are polyploids in holocentric lineages based on chromosome count data alone. Furthermore, it is unclear how differences in genome size and ploidy levels relate to environmental correlates within holocentric lineages, such as the Cyperaceae. METHODS We focus our analyses on tribe Schoeneae, and more specifically the southern African clade of Schoenus. We examine broad-scale patterns of genome size evolution in tribe Schoeneae and focus more intensely on determining the prevalence of polyploidy across the southern African Schoenus by inferring ploidy level with the program ChromEvol, as well as interpreting chromosome number and genome size data. We further investigate whether there are relationships between genome size/ploidy level and environmental variables across the nutrient-poor and summer-arid Cape biodiversity hotspot. KEY RESULTS Our results show a large increase in genome size, but not chromosome number, within Schoenus compared to other species in tribe Schoeneae. Across Schoenus, there is a positive relationship between chromosome number and genome size, and our results suggest that polyploidy is a relatively common process throughout the southern African Schoenus. At the regional scale of the Cape, we show that polyploids are more often associated with drier locations that have more variation in precipitation between dry and wet months, but these results are sensitive to the classification of ploidy level. CONCLUSIONS Polyploidy is relatively common in the southern African Schoenus, where a positive relationship is observed between chromosome number and genome size. Thus, there may be a high incidence of polyploidy in holocentric plants, whose cell division properties differ from monocentrics.
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Affiliation(s)
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Petr Bureš
- Masaryk University, Faculty of Science, Department of Botany and Zoology, Kotlarska 2, Brno, Czech Republic
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Planta J, Liang YY, Xin H, Chansler MT, Prather LA, Jiang N, Jiang J, Childs KL. Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus. G3 GENES|GENOMES|GENETICS 2022; 12:6670624. [PMID: 35976112 PMCID: PMC9526063 DOI: 10.1093/g3journal/jkac211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/18/2022] [Indexed: 12/03/2022]
Abstract
The majority of sequenced genomes in the monocots are from species belonging to Poaceae, which include many commercially important crops. Here, we expand the number of sequenced genomes from the monocots to include the genomes of 4 related cyperids: Carex cristatella and Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from Juncaceae. The high-quality, chromosome-scale genome sequences from these 4 cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Some members of the Cyperaceae and Juncaceae are known to possess holocentric chromosomes. We examined the repeat landscapes in our sequenced genomes to search for potential repeats associated with centromeres. Several large satellite repeat families, comprising 3.2–9.5% of our sequenced genomes, showed dispersed distribution of large satellite repeat clusters across all Carex chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large Juncus satellite repeats were clustered in a single location on each chromosome, with sporadic instances of large satellite repeats throughout the Juncus genomes. Recognizable transposable elements account for about 20% of each of the 4 genome assemblies, with the Carex genomes containing more DNA transposons than retrotransposons while the converse is true for the Juncus genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots.
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Affiliation(s)
- Jose Planta
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
- National Institute of Molecular Biology and Biotechnology, University of the Philippines , Diliman, Quezon City 1101, Philippines
| | - Yu-Ya Liang
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
| | - Haoyang Xin
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
| | - Matthew T Chansler
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
| | - L Alan Prather
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, MSU AgBioResearch, Michigan State University , East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
- Department of Horticulture, MSU AgBioResearch, Michigan State University , East Lansing, MI 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University , East Lansing, MI 48824, USA
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6
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Hodel RGJ, Massatti R, Knowles LL. Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges. Mol Ecol 2022; 31:3722-3737. [PMID: 35560840 PMCID: PMC9327521 DOI: 10.1111/mec.16502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.
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Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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7
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Yoshida K, Kitano J. Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology. PLoS Genet 2021; 17:e1009502. [PMID: 33861748 PMCID: PMC8081341 DOI: 10.1371/journal.pgen.1009502] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 04/28/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a probabilistic model of karyotype evolution based on the "karyograph", which treats karyotype evolution as a walk on the two-dimensional space representing the chromosome and arm numbers. This model enables analysis of the stationary distribution with a stable karyotype for any given parameter. After evaluating their performance using simulated data, we applied our model to two large taxonomic groups of fish, Eurypterygii and series Otophysi, to perform maximum likelihood estimation of the transition rates and reconstruct the evolutionary history of karyotypes. The two taxa significantly differed in the evolution of arm number. The inclusion of speciation and extinction rates demonstrated possibly high extinction rates in species with karyotypes other than the most typical karyotype in both groups. Finally, we made a model including polyploidization rates and applied it to a small plant group. Thus, the use of this probabilistic model can contribute to a better understanding of tempo and mode in karyotype evolution and its possible role in speciation and extinction.
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Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
- * E-mail:
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8
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Hodel RGJ, Massatti R, Bishop SGD, Knowles LL. Testing which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species. Evolution 2021; 75:349-364. [PMID: 33386752 DOI: 10.1111/evo.14159] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/02/2020] [Accepted: 12/16/2020] [Indexed: 11/30/2022]
Abstract
Co-distributed species may exhibit similar phylogeographic patterns due to shared environmental factors or discordant patterns attributed to the influence of species-specific traits. Although either concordant or discordant patterns could occur due to chance, stark differences in key traits (e.g., dispersal ability) may readily explain differences between species. Multiple species' attributes may affect genetic patterns, and it is difficult to isolate the contribution of each. Here we compare the relative importance of two attributes, range size, and niche breadth, in shaping the spatial structure of genetic variation in four sedge species (genus Carex) from the Rocky Mountains. Within two pairs of co-distributed species, one species exhibits narrow niche breadth, while the other species has broad niche breadth. Furthermore, one pair of co-distributed species has a large geographical distribution, while the other has a small distribution. The four species represent a natural experiment to tease apart how these attributes (i.e., range size and niche breadth) affect phylogeographic patterns. Investigations of genetic variation and structure revealed that range size, but not niche breadth, is related to spatial genetic covariation across species of montane sedges. Our study highlights how isolating key attributes across multiple species can inform their impact on processes driving intraspecific differentiation.
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Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, Biological Sciences Building, University of Michigan, Ann Arbor, Michigan, 48109.,Present Address: Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, 20013
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, 86001
| | - Sasha G D Bishop
- Department of Ecology and Evolutionary Biology, Biological Sciences Building, University of Michigan, Ann Arbor, Michigan, 48109
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Biological Sciences Building, University of Michigan, Ann Arbor, Michigan, 48109
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Mayrose I, Lysak MA. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biol Evol 2020; 13:5923296. [PMID: 33566095 PMCID: PMC7875004 DOI: 10.1093/gbe/evaa220] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
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Affiliation(s)
- Itay Mayrose
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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10
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Chromosome numbers of Carex (Cyperaceae) and their taxonomic implications. PLoS One 2020; 15:e0228353. [PMID: 32040511 PMCID: PMC7010274 DOI: 10.1371/journal.pone.0228353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/13/2020] [Indexed: 02/02/2023] Open
Abstract
Counting chromosomes is the first step towards a better understanding of the karyotype evolution and the role of chromosome evolution in species diversification within Carex; however, the chromosome count is not known yet for numerous sedges. In this paper chromosome counts were performed for 23 Carex taxa from Armenia, Austria, the Czech Republic, and Poland. Chromosome numbers were determined for the first time in three species (Carex cilicica, 2n = 54; C. phyllostachys, 2n = 56; C. randalpina, 2n = 78), two subspecies (C. muricata subsp. ashokae, 2n = 58; C. nigra subsp. transcaucasica, 2n = 84) and two hybrids (C. ×decolorans, 2n = 74; C. ×walasii, 2n = 108). Among the taxa whose number of chromosomes had been known before, the largest difference was found in C. hartmaniorum (here 2n = 52) and C. aterrima subsp. medwedewii (here 2n = 52). A difference in the chromosome count was demonstrated for C. cilicica (2n = 54) versus the species of the section Aulocystis (2n = 30 to 40) and for C. tomentosa (2n = 48) versus the species of the section Acrocystis (2n = 18 to 38). The results of this study indicate that the position of C. cilicica in Aulocystis section may raise doubts. Attention was paid to the relationship between C. phyllostachys and taxa of the subgenus Carex section Gynobasidae.
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Burchardt P, Buddenhagen CE, Gaeta ML, Souza MD, Marques A, Vanzela ALL. Holocentric Karyotype Evolution in Rhynchospora Is Marked by Intense Numerical, Structural, and Genome Size Changes. FRONTIERS IN PLANT SCIENCE 2020; 11:536507. [PMID: 33072141 PMCID: PMC7533669 DOI: 10.3389/fpls.2020.536507] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/21/2020] [Indexed: 05/07/2023]
Abstract
Cyperaceae is a family of Monocotyledons comprised of species with holocentric chromosomes that are associated with intense dysploidy and polyploidy events. Within this family the genus Rhynchospora has recently become the focus of several studies that characterize the organization of the holocentric karyotype and genome structures. To broaden our understanding of genome evolution in this genus, representatives of Rhynchospora were studied to contrast chromosome features, C-CMA/DAPI band distribution and genome sizes. Here, we carried out a comparative analysis for 35 taxa of Rhynchospora, and generated new genome size estimates for 20 taxa. The DNA 2C-values varied up to 22-fold, from 2C = 0.51 pg to 11.32 pg, and chromosome numbers ranged from 2n = 4 to 61. At least 37% of our sampling exhibited 2n different from the basic number x = 5, and chromosome rearrangements were also observed. A large variation in C-CMA/DAPI band accumulation and distribution was observed as well. We show that genome variation in Rhynchospora is much larger than previously reported. Phylogenetic analysis showed that most taxa were grouped in clades corresponding to previously described taxonomic sections. Basic chromosome numbers are the same within every section, however, changes appeared in all the clades. Ancestral chromosome number reconstruction revealed n = 5 as the most likely ancestral complements, but n = 10 appears as a new possibility. Chromosome evolution models point to polyploidy as the major driver of chromosome evolution in Rhynchospora, followed by dysploidy. A negative correlation between chromosome size and diploid number open the discussion for holokinetic drive-based genome evolution. This study explores relationships between karyotype differentiation and genome size variation in Rhynchospora, and contrasts it against the phylogeny of this holocentric group.
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Affiliation(s)
- Paula Burchardt
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Marcos L. Gaeta
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
| | - Murilo D. Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- *Correspondence: André L. L. Vanzela, ; André Marques,
| | - André L. L. Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina, Londrina, Brazil
- *Correspondence: André L. L. Vanzela, ; André Marques,
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Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae). Mol Phylogenet Evol 2019; 135:203-209. [DOI: 10.1016/j.ympev.2019.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 11/20/2022]
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13
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Chung KS, Hoshino T, Masaki T, Im HT, Ji SJ. Chromosome Counts of Six Korean Carex Species (Cyperaceae). CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Takuji Hoshino
- Department of Biosphere-Geosphere Science, Faculty of Biosphere-Geosphere Science, Okayama University of Science
| | - Tomomi Masaki
- Department of Biosphere-Geosphere Science, Faculty of Biosphere-Geosphere Science, Okayama University of Science
| | - Hyoung-Tak Im
- Department of Division of Biological Science, Chonnam National University
| | - Seong-Jin Ji
- Facility Management Division, National Science Museum
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14
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Carta A, Bedini G, Peruzzi L. Unscrambling phylogenetic effects and ecological determinants of chromosome number in major angiosperm clades. Sci Rep 2018; 8:14258. [PMID: 30250220 PMCID: PMC6155329 DOI: 10.1038/s41598-018-32515-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/10/2018] [Indexed: 11/09/2022] Open
Abstract
As variations in the chromosome number are recognized to be of evolutionary interest but are also widely debated in the literature, we aimed to quantitatively test for possible relationships among the chromosome number, plant traits, and environmental factors. In particular, the chromosome number and drivers of its variation were examined in 801 Italian endemic vascular plants, for a total of 1364 accessions. We estimated phylogenetic inertia and adaptation in chromosome number - based on an Ornstein-Uhlenbeck process - and related chromosome numbers with other plant traits and environmental variables. Phylogenetic effects in chromosome number varied among the examined clades but were generally high. Chromosome numbers were poorly related to large scale climatic conditions, while a stronger relationship with categorical variables was found. Specifically, open, disturbed, drought-prone habitats selected for low chromosome numbers, while perennial herbs, living in shaded, stable environments were associated with high chromosome numbers. Altogether, our findings support an evolutionary role of chromosome number variation, and we argue that environmental stability favours higher recombination rates in comparison to unstable environments. In addition, by comparing the results of models testing for the evolvability of 2n and of x, we provide insight into the presumptive ecological significance of polyploidy.
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Affiliation(s)
- Angelino Carta
- Department of Biology, Unit of Botany, University of Pisa, via Derna 1, 56126, Pisa, Italy.
| | - Gianni Bedini
- Department of Biology, Unit of Botany, University of Pisa, via Derna 1, 56126, Pisa, Italy
| | - Lorenzo Peruzzi
- Department of Biology, Unit of Botany, University of Pisa, via Derna 1, 56126, Pisa, Italy
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15
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Escudero M, Hahn M, Hipp AL. RAD-seq linkage mapping and patterns of segregation distortion in sedges: meiosis as a driver of karyotypic evolution in organisms with holocentric chromosomes. J Evol Biol 2018; 31:833-843. [PMID: 29573004 DOI: 10.1111/jeb.13267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/08/2018] [Accepted: 03/08/2018] [Indexed: 12/12/2022]
Abstract
Meiotic drive, the class of meiotic mechanisms that drive unequal segregation of alleles among gametes, may be an important force in karyotype evolution. Its role in holocentric organisms, whose chromosomes lack localized centromeres, is poorly understood. We crossed two individuals of Carex scoparia (Cyperaceae) with different chromosome numbers (2n = 33II = 66 × 2n = 32II = 64) to obtain F1 individuals, which we then self-pollinated to obtain second-generation (F2) crosses. RAD-seq was performed for 191 individuals (including the parents, five F1 individuals and 184 F2 individuals). Our F2 linkage map based on stringent editing of the RAD-seq data set yielded 32 linkage groups. In the final map, 865 loci were located on a linkage map of 3966.99 cM (linkage groups ranged from 24.39 to 193.31 cM in length and contained 5-51 loci each). Three linkage groups exhibit more loci under segregation distortion than expected by chance; within linkage groups, loci exhibiting segregation distortion are clustered. This finding implicates meiotic drive in the segregation of chromosome variants, suggesting that selection of chromosome variants in meiosis may contribute to the establishment and fixation of chromosome variants in Carex, which is renowned for high chromosomal and species diversity. This is an important finding as previous studies demonstrate that chromosome divergence may play a key role in differentiation and speciation in Carex.
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Affiliation(s)
- Marcial Escudero
- The Morton Arboretum, Lisle, IL, USA.,Botany Department, Field Museum of Natural History, Chicago, IL, USA.,Department of Plant Biology and Ecology, Universidad de Sevilla, Sevilla, Spain
| | | | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL, USA.,Botany Department, Field Museum of Natural History, Chicago, IL, USA
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16
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Mandáková T, Lysak MA. Post-polyploid diploidization and diversification through dysploid changes. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:55-65. [PMID: 29567623 DOI: 10.1016/j.pbi.2018.03.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 05/06/2023]
Abstract
Whole-genome duplications are widespread across land plant phylogenies and particularly frequent in ferns and angiosperms. Genome duplications spurred the evolution of key innovations associated with diversification in many angiosperm clades and lineages. Such diversifications are not initiated by genome doubling per se. Rather, differentiation of the primary polyploid populations through a range of processes results in post-polyploid genome diploidization. Structural diploidization gradually reverts the polyploid genome to one functionally diploid-like through chromosomal rearrangements which frequently result in dysploid changes. Dysploidies may lead to reproductive isolation among post-polyploid offspring and significantly contribute to speciation and cladogenetic events.
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Affiliation(s)
- Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic.
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17
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Freyman WA, Höhna S. Cladogenetic and Anagenetic Models of Chromosome Number Evolution: A Bayesian Model Averaging Approach. Syst Biol 2018; 67:195-215. [PMID: 28945917 DOI: 10.1093/sysbio/syx065] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 07/01/2017] [Indexed: 11/14/2022] Open
Abstract
ABSSTRACT Chromosome number is a key feature of the higher-order organization of the genome, and changes in chromosome number play a fundamental role in evolution. Dysploid gains and losses in chromosome number, as well as polyploidization events, may drive reproductive isolation and lineage diversification. The recent development of probabilistic models of chromosome number evolution in the groundbreaking work by Mayrose et al. (2010, ChromEvol) have enabled the inference of ancestral chromosome numbers over molecular phylogenies and generated new interest in studying the role of chromosome changes in evolution. However, the ChromEvol approach assumes all changes occur anagenetically (along branches), and does not model events that are specifically cladogenetic. Cladogenetic changes may be expected if chromosome changes result in reproductive isolation. Here we present a new class of models of chromosome number evolution (called ChromoSSE) that incorporate both anagenetic and cladogenetic change. The ChromoSSE models allow us to determine the mode of chromosome number evolution; is chromosome evolution occurring primarily within lineages, primarily at lineage splitting, or in clade-specific combinations of both? Furthermore, we can estimate the location and timing of possible chromosome speciation events over the phylogeny. We implemented ChromoSSE in a Bayesian statistical framework, specifically in the software RevBayes, to accommodate uncertainty in parameter estimates while leveraging the full power of likelihood based methods. We tested ChromoSSE's accuracy with simulations and re-examined chromosomal evolution in Aristolochia, Carex section Spirostachyae, Helianthus, Mimulus sensu lato (s.l.), and Primula section Aleuritia, finding evidence for clade-specific combinations of anagenetic and cladogenetic dysploid and polyploid modes of chromosome evolution. [Anagenetic; Bayes factors; chromosome evolution; chromosome speciation; chromoSSE; cladogenetic; dysploidy; phylogenetic models; polyploidy; reversible-jump Markov chain Monte Carlo; whole genome duplication.].
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Affiliation(s)
- William A Freyman
- Department of Integrative Biology, University of California, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA
| | - Sebastian Höhna
- Department of Integrative Biology, University of California, 3040 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA.,Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA 94720, USA
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18
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Ribeiro T, Buddenhagen CE, Thomas WW, Souza G, Pedrosa-Harand A. Are holocentrics doomed to change? Limited chromosome number variation in Rhynchospora Vahl (Cyperaceae). PROTOPLASMA 2018; 255:263-272. [PMID: 28844108 DOI: 10.1007/s00709-017-1154-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/14/2017] [Indexed: 05/23/2023]
Abstract
Karyotype evolution in species with non-localised centromeres (holocentric chromosomes) is usually very dynamic and associated with recurrent fission and fusion (also termed agmatoploidy/symploidy) events. In Rhynchospora (Cyperaceae), one of the most species-rich sedge genera, all analysed species have holocentric chromosomes and their numbers range from 2n = 4 to 2n = 84. Agmatoploidy/symploidy and polyploidy were suggested as the main processes in the reshuffling of Rhynchospora karyotypes, although testing different scenarios of chromosome number evolution in a phylogenetic framework has not been attempted until now. Here, we used maximum likelihood and model-based analyses, in combination with genome size estimation and ribosomal DNA distribution, to understand chromosome evolution in Rhynchospora. Overall, chromosome number variation showed a significant phylogenetic signal and the majority of the lineages maintained a karyotype of 2n = 10 (~48% of the species), the most likely candidate for the ancestral number of the genus. Higher and lower chromosome numbers were restricted to specific clades, whilst polyploidy and/or fusion/fission events were present in specific branches. Variation in genome size and ribosomal DNA site number showed no correlation with ploidy level or chromosome number. Although different mechanisms of karyotype evolution (polyploidy, fusion and fission) seem to be acting in distinct lineages, the degree of chromosome variation and the main mechanisms involved are comparable to those found in some monocentric genera and lower than expected for a holocentric genus.
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Affiliation(s)
- Tiago Ribeiro
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | | | | | - Gustavo Souza
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Departamento de Botânica, Centro de Biociências, Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Cidade Universitária, Recife, PE, 50670-901, Brazil.
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19
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Do holocentric chromosomes represent an evolutionary advantage? A study of paired analyses of diversification rates of lineages with holocentric chromosomes and their monocentric closest relatives. Chromosome Res 2017; 26:139-152. [PMID: 29043597 DOI: 10.1007/s10577-017-9566-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022]
Abstract
Despite most of the cytogenetic research is focused on monocentric chromosomes, chromosomes with kinetochoric activity localized in a single centromere, several studies have been centered on holocentric chromosomes which have diffuse kinetochoric activity along the chromosomes. The eukaryotic organisms that present this type of chromosomes have been relatively understudied despite they constitute rather diversified species lineages. On the one hand, holocentric chromosomes may present intrinsic benefits (chromosome mutations such as fissions and fusions are potentially neutral in holocentrics). On the other hand, they present restrictions to the spatial separation of the functions of recombination and segregation during meiotic divisions (functions that may interfere), separation that is found in monocentric chromosomes. In this study, we compare the diversification rates of all known holocentric lineages in animals and plants with their most related monocentric lineages in order to elucidate whether holocentric chromosomes constitute an evolutionary advantage in terms of diversification and species richness. The results showed that null hypothesis of equal mean diversification rates cannot be rejected, leading us to surmise that shifts in diversification rates between holocentric and monocentric lineages might be due to other factors, such as the idiosyncrasy of each lineage or the interplay of evolutionary selections with the benefits of having either monocentric or holocentric chromosomes.
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20
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Vershinina AO, Lukhtanov VA. Evolutionary mechanisms of runaway chromosome number change in Agrodiaetus butterflies. Sci Rep 2017; 7:8199. [PMID: 28811556 PMCID: PMC5557896 DOI: 10.1038/s41598-017-08525-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/10/2017] [Indexed: 11/17/2022] Open
Abstract
Despite predictions of the classic, hybrid-sterility model of chromosomal speciation, some organisms demonstrate high rate of karyotype evolution. This rate is especially impressive in Agrodiaetus butterflies that rapidly evolved the greatest chromosome number diversity known in animal kingdom within a single subgenus. Here we analyzed karyotype evolution in Agrodiaetus using phylogenetic comparative methods. We found that chromosome numbers possess a strong phylogenetic signal. This disproves the chromosome megaevolution model that proposes multiple chromosome rearrangements to accumulate independently in each of closely related species. We found that Brownian motion gives a more adequate description of observed trait changes than Ornstein-Uhlenbeck model. This indicates that chromosome numbers evolve via random walk along branches of the phylogeny. We discovered a correlation between karyotype changes and phylogeny branch lengths. This gradual pattern is inconsistent with the hybrid-sterility model which, due to association of major chromosome changes with cladogenetic events, predicts a high degree of punctualism in karyotype evolution. Thus, low underdominace of chromosomal rearrangements and/or prevalence of the recombination-suppression model over the hybrid-sterility model of chromosome speciation are the most common engines of the runaway chromosome number change observed.
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Affiliation(s)
- Alisa O Vershinina
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia.
- Department of Ecology & Evolutionary Biology, University of California Santa Cruz, 95064, Santa Cruz, CA, USA.
| | - Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034, St. Petersburg, Russia.
- Department of Entomology, St Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia.
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21
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Chenuil A, Saucède T, Hemery LG, Eléaume M, Féral JP, Améziane N, David B, Lecointre G, Havermans C. Understanding processes at the origin of species flocks with a focus on the marine Antarctic fauna. Biol Rev Camb Philos Soc 2017; 93:481-504. [DOI: 10.1111/brv.12354] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 06/20/2017] [Accepted: 06/27/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Anne Chenuil
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE-UMR7263); Aix-Marseille Univ, Univ Avignon, CNRS, IRD, Station Marine d'Endoume, Chemin de la Batterie des Lions; F-13007 Marseille France
| | - Thomas Saucède
- UMR6282 Biogéosciences; CNRS - Université de Bourgogne Franche-Comté, 6 boulevard Gabriel; F-21000 Dijon France
| | - Lenaïg G. Hemery
- DMPA, UMR 7208 BOREA/MNHN/CNRS/Paris VI/ Univ Caen, 57 rue Cuvier; 75231 Paris Cedex 05 France
| | - Marc Eléaume
- UMR7205 Institut de Systématique; Evolution et Biodiversité, CNRS-MNHN-UPMC-EPHE, CP 24, Muséum national d'Histoire naturelle, 57 rue Cuvier; 75005 Paris France
| | - Jean-Pierre Féral
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE-UMR7263); Aix-Marseille Univ, Univ Avignon, CNRS, IRD, Station Marine d'Endoume, Chemin de la Batterie des Lions; F-13007 Marseille France
| | - Nadia Améziane
- UMR7205 Institut de Systématique; Evolution et Biodiversité, CNRS-MNHN-UPMC-EPHE, CP 24, Muséum national d'Histoire naturelle, 57 rue Cuvier; 75005 Paris France
| | - Bruno David
- UMR6282 Biogéosciences; CNRS - Université de Bourgogne Franche-Comté, 6 boulevard Gabriel; F-21000 Dijon France
- Muséum national d'Histoire naturelle, 57 rue Cuvier; 75005 Paris France
| | - Guillaume Lecointre
- UMR7205 Institut de Systématique; Evolution et Biodiversité, CNRS-MNHN-UPMC-EPHE, CP 24, Muséum national d'Histoire naturelle, 57 rue Cuvier; 75005 Paris France
| | - Charlotte Havermans
- Marine Zoology, Bremen Marine Ecology (BreMarE); University of Bremen, PO Box 330440; 28334 Bremen Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12; D-27570 Bremerhaven Germany
- OD Natural Environment; Royal Belgian Institute of Natural Sciences, Rue Vautier 29; B-1000 Brussels Belgium
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22
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Chung KS, Hoshino T, Masaki T, Im HT. Cytological Investigations on Eight <i>Carex</i> Species in Korea (Cyperaceae). CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Takuji Hoshino
- Department of Biosphere-Geosphere Science, Faculty of Biosphere-Geosphere Science, Okayama University of Science
| | - Tomomi Masaki
- Department of Biosphere-Geosphere Science, Faculty of Biosphere-Geosphere Science, Okayama University of Science
| | - Hyoung-Tak Im
- Department of Division of Biological Science, Chonnam National University
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23
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M. Pedersen AT, Nowak MD, Brysting AK, Elven R, Bjorå CS. Hybrid Origins of Carex rostrata var. borealis and C. stenolepis, Two Problematic Taxa in Carex Section Vesicariae (Cyperaceae). PLoS One 2016; 11:e0165430. [PMID: 27780239 PMCID: PMC5079627 DOI: 10.1371/journal.pone.0165430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/11/2016] [Indexed: 11/19/2022] Open
Abstract
Hybridization is frequent in the large and ecologically significant genus Carex (Cyperaceae). In four important sections of the northern regions (Ceratocystis, Glareosae, Phacocystis and Vesicariae), the frequent occurrence of hybrids often renders the identification of "pure" species and hybrids difficult. In this study we address the origins and taxonomic rank of two taxa of section Vesicariae: Carex rostrata var. borealis and C. stenolepis. The origin and taxonomic status of C. stenolepis has been the subject of substantial debate over the years, whereas C. rostrata var. borealis has received very little attention in the years since its first description in the 19th century. By performing an extensive sampling of relevant taxa from a broad distribution range, and analyzing data from fifteen microsatellite loci developed specifically for our study together with pollen stainability measures, we resolve the hybrid origins of C. rostrata var. borealis and C. stenolepis and provide new insights into this taxonomically challenging group of sedges. Our results are in accordance with previous findings suggesting that C. stenolepis is a hybrid between C. vesicaria and C. saxatilis. They are also in accordance with a previous proposition that C. rostrata var. borealis is a hybrid between C. rostrata and C. rotundata, and furthermore suggest that both hybrids are the result of multiple, recent (i.e., postglacial) hybridization events. We found little evidence for successful sexual reproduction within C. rostrata var. borealis and C. stenolepis, but conclude that the common and recurrent, largely predictable occurrence of these taxa justifies accepting both hybrids as hybrid species with binomial names. There are, however, complications as to types and priority names, and we therefore choose to address these problems in a separate paper.
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Affiliation(s)
| | | | - Anne K. Brysting
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Reidar Elven
- Natural History Museum, University of Oslo, Oslo, Norway
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24
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McCann J, Schneeweiss GM, Stuessy TF, Villaseñor JL, Weiss-Schneeweiss H. The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae). PLoS One 2016; 11:e0162299. [PMID: 27611687 PMCID: PMC5017664 DOI: 10.1371/journal.pone.0162299] [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: 04/29/2016] [Accepted: 08/20/2016] [Indexed: 01/13/2023] Open
Abstract
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.
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Affiliation(s)
- Jamie McCann
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
- * E-mail:
| | - Tod F. Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
- Herbarium, Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Ave., 43210 Columbus, Ohio, United States of America
| | - Jose L. Villaseñor
- Instituto de Biologia, Departamento de Botánica, Universidad Nacional Autónoma de México, Tercer Circuito s/n Ciudad Universitaria Delegación Coyoacán Apartado Postal 70-233, 04510 México, D.F., México
| | - Hanna Weiss-Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
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25
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Gorelick R, Carpinone J, Derraugh LJ. No universal differences between female and male eukaryotes: anisogamy and asymmetrical female meiosis. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12874] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Root Gorelick
- Department of Biology; Carleton University; 1125 Raven Road Ottawa Ontario K1S 5B6 Canada
- School of Mathematics & Statistics and Institute of Interdisciplinary Studies; Carleton University; 1125 Raven Road Ottawa Ontario K1S 5B6 Canada
| | - Jessica Carpinone
- Department of Biology; Carleton University; 1125 Raven Road Ottawa Ontario K1S 5B6 Canada
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26
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Escudero M, Hahn M, Brown BH, Lueders K, Hipp AL. Chromosomal rearrangements in holocentric organisms lead to reproductive isolation by hybrid dysfunction: The correlation between karyotype rearrangements and germination rates in sedges. AMERICAN JOURNAL OF BOTANY 2016; 103:1529-36. [PMID: 27558707 DOI: 10.3732/ajb.1600051] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/14/2016] [Indexed: 05/13/2023]
Abstract
PREMISE OF THE STUDY Understanding the drivers of speciation is a central task of evolutionary biology. Chromosomal rearrangements are known to play an important role in species diversification, but the role of rearrangements of holocentric chromosomes-chromosomes without localized centromeres-is poorly understood. METHODS We made numerous artificial crosses between Carex scoparia individuals of different diploid chromosome numbers and, for comparison, between individuals of the same chromosome number. We studied chromosome pairing and chromosomal rearrangements in the F1 individuals using light microscopy. We then estimated germination rates as a function of geographic distance, genetic distance, chromosome number differences in parents, and pairing irregularities in F1 individuals, using generalized least squares to fit alternative regression models. KEY RESULTS The most informative predictors of germination rates in the F1 generation are chromosome number differences and minimum number of chromosome pairing irregularities in the F1 individuals. Genetic and geographic distances between parents are not significant predictors. CONCLUSIONS Holocentric chromosomal rearrangements play an important role in postzygotic reproductive isolation in Carex through F1 hybrid inviability and sterility. Hybrid dysfunction seems to be a suitable model for chromosomal speciation when there are several chromosomal rearrangements between parents. However, we have not tested the hypothesis that genome rearrangements may also play an important role in suppressing recombination between cytogenetically divergent populations.
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Affiliation(s)
- Marcial Escudero
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, Illinois 60532 USA Department of Botany, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois 60605 USA Department of Plant Biology and Ecology, University of Seville, Reina Mercedes sn 41010 Seville, Spain.
| | - Marlene Hahn
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, Illinois 60532 USA
| | - Bethany H Brown
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, Illinois 60532 USA
| | - Kate Lueders
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, Illinois 60532 USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, Illinois 60532 USA Department of Botany, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois 60605 USA
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27
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Chung KS, Hoshino T, Masaki T, Yang JC, Im HT. Cytological Studies on Seven Species of Korean Carex (Cyperaceae). CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.143] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Takuji Hoshino
- Department of Biosphere-Geosphere Science, Faculty of Biosphere-Geosphere Science, Okayama University of Science
| | - Tomomi Masaki
- Department of Biosphere-Geosphere Science, Faculty of Biosphere-Geosphere Science, Okayama University of Science
| | | | - Hyoung-Tak Im
- Department of division of Biological Science, Chonnam National University
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28
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Kaliontzopoulou A, Adams DC. Phylogenies, the Comparative Method, and the Conflation of Tempo and Mode. Syst Biol 2015; 65:1-15. [DOI: 10.1093/sysbio/syv079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/07/2015] [Indexed: 11/15/2022] Open
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29
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Escudero M, Maguilla E, Loureiro J, Castro M, Castro S, Luceño M. Genome size stability despite high chromosome number variation in Carex gr. laevigata. AMERICAN JOURNAL OF BOTANY 2015; 102:233-8. [PMID: 25667076 DOI: 10.3732/ajb.1400433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
PREMISE OF THE STUDY In organisms with holocentric chromosomes like Carex species, chromosome number evolution has been hypothesized to be a result of fission, fusion, and/or translocation events. Negative, positive, or the absence of correlations have been found between chromosome number and genome size in Carex. METHODS Using the inferred diploid chromosome number and 80 genome size measurements from 26 individuals and 20 populations of Carex gr. laevigata, we tested the null hypothesis of chromosome number evolution by duplication and deletion of whole chromosomes. KEY RESULTS Our results show a significant positive correlation between genome size and chromosome number, but the slope of such correlation supports the hypothesis of proliferation and removal of repetitive DNA fragments to explain genome size variation rather than duplication and deletion of whole chromosomes. CONCLUSIONS Our results refine the theory of the holokinetic drive: this mechanism is proposed to facilitate repetitive DNA removal (or any segmental deletion) when smaller homologous chromosomes are preferentially inherited, or repetitive DNA proliferation (or any segmental duplication) when larger homologs are preferred. This study sheds light on how karyotype evolution plays an important role in the diversification of the species of the genus Carex.
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Affiliation(s)
- Marcial Escudero
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Americo Vespucio sn 41092 Seville, Spain
| | - Enrique Maguilla
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Carretera de Utrera Km 1 sn 41013 Seville, Spain
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Modesto Luceño
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Carretera de Utrera Km 1 sn 41013 Seville, Spain
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Escudero M, Eaton DA, Hahn M, Hipp AL. Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae). Mol Phylogenet Evol 2014; 79:359-67. [DOI: 10.1016/j.ympev.2014.06.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/19/2014] [Accepted: 06/30/2014] [Indexed: 11/27/2022]
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Bureš P, Zedek F. Holokinetic drive: centromere drive in chromosomes without centromeres. Evolution 2014; 68:2412-20. [PMID: 24758327 DOI: 10.1111/evo.12437] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 04/13/2014] [Indexed: 02/02/2023]
Abstract
Similar to how the model of centromere drive explains the size and complexity of centromeres in monocentrics (organisms with localized centromeres), our model of holokinetic drive is consistent with the divergent evolution of chromosomal size and number in holocentrics (organisms with nonlocalized centromeres) exhibiting holokinetic meiosis (holokinetics). Holokinetic drive is proposed to facilitate chromosomal fission and/or repetitive DNA removal (or any segmental deletion) when smaller homologous chromosomes are preferentially inherited or chromosomal fusion and/or repetitive DNA proliferation (or any segmental duplication) when larger homologs are preferred. The hypothesis of holokinetic drive is supported primarily by the negative correlation between chromosome number and genome size that is documented in holokinetic lineages. The supporting value of two older cross-experiments on holokinetic structural heterozygotes (the rush Luzula elegans and butterflies of the genus Antheraea) that indicate the presence of size-preferential homolog transmission via female meiosis for holokinetic drive is discussed, along with the further potential consequences of holokinetic drive in comparison with centromere drive.
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Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
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Parallel and convergent diversification in two northern hemispheric species-rich Carex lineages (Cyperaceae). ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0171-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Arrigo N, Therrien J, Anderson CL, Windham MD, Haufler CH, Barker MS. A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys. AMERICAN JOURNAL OF BOTANY 2013; 100:1672-82. [PMID: 23935110 DOI: 10.3732/ajb.1200426] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. METHODS Our study included most Tetragonostachys species, using plastid and nuclear sequences, fossil and herbarium records, and climate variables to describe the species diversity, phylogenetic relationships, divergence times, and climatic niche evolution in the subgenus. KEY RESULTS We found that subgenus Tetragonostachys forms a monophyletic group sister to Selaginella lepidophylla and may have diverged from other Selaginella because of a Gondwanan-Laurasian vicariance event ca. 240 mya. The North American radiation of Tetragonostachys appears to be much more recent and to have occurred during the Early Cretaceous-late Paleocene interval. We identified two significant and nested ecological niche shifts during the evolution of Tetragonostachys associated with extreme drought tolerance and a more recent shift to cold climates. Our analyses suggest that drought tolerance evolved in the warm deserts of southwest North America and may have been advantageous for colonization of cold and dry boreal climates. CONCLUSIONS Our investigation provides a foundation for future research addressing the genomics of ecological niche evolution and the potential role of reticulate evolution in Selaginella subgenus Tetragonostachys.
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Affiliation(s)
- Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, P.O. Box 210088, Tucson, Arizona 85721, USA
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Escudero M, Weber JA, Hipp AL. Species coherence in the face of karyotype diversification in holocentric organisms: the case of a cytogenetically variable sedge (Carex scoparia, Cyperaceae). ANNALS OF BOTANY 2013; 112:515-26. [PMID: 23723260 PMCID: PMC3718211 DOI: 10.1093/aob/mct119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The sedge genus Carex, the most diversified angiosperm genus of the northern temperate zone, is renowned for its holocentric chromosomes and karyotype variability. The genus exhibits high variation in chromosome numbers both among and within species. Despite the possibility that this chromosome evolution may play a role in the high species diversity of Carex, population-level patterns of molecular and cytogenetic differentiation in the genus have not been extensively studied. METHODS Microsatellite variation (11 loci, 461 individuals) and chromosomal diversity (82 individuals) were investigated in 22 Midwestern populations of the North American sedge Carex scoparia and two Northeastern populations. KEY RESULTS Among Midwestern populations, geographic distance is the most important predictor of genetic differentiation. Within populations, inbreeding is high and chromosome variation explains a significant component of genetic differentiation. Infrequent dispersal among populations separated by >100 km explains an important component of molecular genetic and cytogenetic diversity within populations. However, karyotype variation and correlation between genetic and chromosomal variation persist within populations even when putative migrants based on genetic data are excluded. CONCLUSIONS These findings demonstrate dispersal and genetic connectivity among widespread populations that differ in chromosome numbers, explaining the phenomenon of genetic coherence in this karyotypically diverse sedge species. More generally, the study suggests that traditional sedge taxonomic boundaries demarcate good species even when those species encompass a high range of chromosomal diversity. This finding is important evidence as we work to document the limits and drivers of biodiversity in one of the world's largest angiosperm genera.
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Affiliation(s)
- Marcial Escudero
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- Pablo de Olavide University, Carretera de Utrera km 1 SN, Seville 41013, Spain
| | - Jaime A. Weber
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
| | - Andrew L. Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
- The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605-2496, USA
- For correspondence. E-mail
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Melters DP, Paliulis LV, Korf IF, Chan SWL. Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis. Chromosome Res 2012; 20:579-93. [PMID: 22766638 DOI: 10.1007/s10577-012-9292-1] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In most eukaryotes, the kinetochore protein complex assembles at a single locus termed the centromere to attach chromosomes to spindle microtubules. Holocentric chromosomes have the unusual property of attaching to spindle microtubules along their entire length. Our mechanistic understanding of holocentric chromosome function is derived largely from studies in the nematode Caenorhabditis elegans, but holocentric chromosomes are found over a broad range of animal and plant species. In this review, we describe how holocentricity may be identified through cytological and molecular methods. By surveying the diversity of organisms with holocentric chromosomes, we estimate that the trait has arisen at least 13 independent times (four times in plants and at least nine times in animals). Holocentric chromosomes have inherent problems in meiosis because bivalents can attach to spindles in a random fashion. Interestingly, there are several solutions that have evolved to allow accurate meiotic segregation of holocentric chromosomes. Lastly, we describe how extensive genome sequencing and experiments in nonmodel organisms may allow holocentric chromosomes to shed light on general principles of chromosome segregation.
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Affiliation(s)
- Daniël P Melters
- Department of Molecular and Cell Biology and Genome Center, University of California, Davis, CA, USA
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Weng ML, Ruhlman TA, Gibby M, Jansen RK. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). Mol Phylogenet Evol 2012; 64:654-70. [DOI: 10.1016/j.ympev.2012.05.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/17/2012] [Accepted: 05/22/2012] [Indexed: 11/28/2022]
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Escudero M, Hipp AL, Hansen TF, Voje KL, Luceño M. Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). THE NEW PHYTOLOGIST 2012; 195:237-47. [PMID: 22489934 DOI: 10.1111/j.1469-8137.2012.04137.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
• Changes in chromosome number as a result of fission and fusion in holocentrics have direct and immediate effects on the recombination rate. We investigate the support for the classic hypothesis that environmental stability selects for increased recombination rates. • We employed a phylogenetic and cytogenetic data set from one of the most diverse angiosperm genera in the world, which has the largest nonpolyploid chromosome radiation (Carex, Cyperaceae; 2n = 12-124; 2100 spp.). We evaluated alternative Ornstein-Uhlenbeck models of chromosome number adaptation to the environment in an information-theoretic framework. • We found moderate support for a positive influence of lateral inflorescence unit size on chromosome number, which may be selected in a stable environment in which resources for reproductive investment are larger. We found weak support for a positive influence on chromosome number of water-saturated soils and among-month temperature constancy, which would be expected to be negatively select for pioneering species. Chromosome number showed a strong phylogenetic signal. • We argue that our finding of small but significant effects of life history and ecology is compatible with our original hypothesis regarding selection of optima in recombination rates: low recombination rate is optimal when inmediate fitness is required. By contrast, high recombination rate is optimal when stable environments allow for evolutionary innovation.
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Affiliation(s)
- Marcial Escudero
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain.
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Inda LA, Pimentel M, Chase MW. Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes. ANNALS OF BOTANY 2012; 110:71-90. [PMID: 22539542 PMCID: PMC3380586 DOI: 10.1093/aob/mcs083] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 03/01/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Tribe Orchideae (Orchidaceae: Orchidoideae) comprises around 62 mostly terrestrial genera, which are well represented in the Northern Temperate Zone and less frequently in tropical areas of both the Old and New Worlds. Phylogenetic relationships within this tribe have been studied previously using only nuclear ribosomal DNA (nuclear ribosomal internal transcribed spacer, nrITS). However, different parts of the phylogenetic tree in these analyses were weakly supported, and integrating information from different plant genomes is clearly necessary in orchids, where reticulate evolution events are putatively common. The aims of this study were to: (1) obtain a well-supported and dated phylogenetic hypothesis for tribe Orchideae, (ii) assess appropriateness of recent nomenclatural changes in this tribe in the last decade, (3) detect possible examples of reticulate evolution and (4) analyse in a temporal context evolutionary trends for subtribe Orchidinae with special emphasis on pollination systems. METHODS The analyses included 118 samples, belonging to 103 species and 25 genera, for three DNA regions (nrITS, mitochondrial cox1 intron and plastid rpl16 intron). Bayesian and maximum-parsimony methods were used to construct a well-supported and dated tree. Evolutionary trends in the subtribe were analysed using Bayesian and maximum-likelihood methods of character evolution. KEY RESULTS The dated phylogenetic tree strongly supported the recently recircumscribed generic concepts of Bateman and collaborators. Moreover, it was found that Orchidinae have diversified in the Mediterranean basin during the last 15 million years, and one potential example of reticulate evolution in the subtribe was identified. In Orchidinae, pollination systems have shifted on numerous occasions during the last 23 million years. CONCLUSIONS The results indicate that ancestral Orchidinae were hymenopteran-pollinated, food-deceptive plants and that these traits have been dominant throughout the evolutionary history of the subtribe in the Mediterranean. Evidence was also obtained that the onset of sexual deception might be linked to an increase in labellum size, and the possibility is discussed that diversification in Orchidinae developed in parallel with diversification of bees and wasps from the Miocene onwards.
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Affiliation(s)
- Luis A Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, carretera de Cuarte s/n., Huesca, Spain.
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Chung KS, Hipp AL, Roalson EH. CHROMOSOME NUMBER EVOLVES INDEPENDENTLY OF GENOME SIZE IN A CLADE WITH NONLOCALIZED CENTROMERES (CAREX: CYPERACEAE). Evolution 2012; 66:2708-22. [DOI: 10.1111/j.1558-5646.2012.01624.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rutkowska J, Lagisz M, Nakagawa S. The long and the short of avian W chromosomes: no evidence for gradual W shortening. Biol Lett 2012; 8:636-8. [PMID: 22417794 DOI: 10.1098/rsbl.2012.0083] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The well-established view of the evolution of sex chromosome dimorphism is of a gradual genetic and morphological degeneration of the hemizygous chromosome. Yet, no large-scale comparative analysis exists to support this view. Here, we analysed karyotypes of 200 bird species to test whether the supposed directional changes occur in bird sex chromosomes. We found no support for the view that W chromosomes gradually become smaller over evolutionary time. On the contrary, the length of the W chromosome can fluctuate over short time scales, probably involving both shortening and elongation of non-coding regions. Recent discoveries of near-identical palindromes and neo-sex chromosomes in birds may also contribute to the observed variation. Further studies are now needed to investigate how chromosome morphology relates to its gene content, and whether the changes in size were driven by selection.
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Affiliation(s)
- Joanna Rutkowska
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland.
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Escudero M, Hipp AL, Waterway MJ, Valente LM. Diversification rates and chromosome evolution in the most diverse angiosperm genus of the temperate zone (Carex, Cyperaceae). Mol Phylogenet Evol 2012; 63:650-5. [PMID: 22366369 DOI: 10.1016/j.ympev.2012.02.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/29/2012] [Accepted: 02/10/2012] [Indexed: 01/13/2023]
Abstract
The sedge family (Cyperaceae: Poales; ca. 5600 spp.) is a hyperdiverse cosmopolitan group with centres of species diversity in Africa, Australia, eastern Asia, North America, and the Neotropics. Carex, with ca. 40% of the species in the family, is one of the most species-rich angiosperm genera and the most diverse in temperate regions of the Northern Hemisphere, making it atypical among plants in that it inverts the latitudinal gradient of species richness. Moreover, Carex exhibits high rates of chromosome rearrangement via fission, fusion, and translocation, which distinguishes it from the rest of the Cyperaceae. Here, we use a phylogenetic framework to examine how the onset of contemporary temperate climates and the processes of chromosome evolution have influenced the diversification dynamics of Carex. We provide estimates of diversification rates and map chromosome transitions across the evolutionary history of the main four clades of Carex. We demonstrate that Carex underwent a shift in diversification rates sometime between the Late Eocene and the Oligocene, during a global cooling period, which fits with a transition in diploid chromosome number. We suggest that adaptive radiation to novel temperate climates, aided by a shift in the mode of chromosome evolution, may explain the large-scale radiation of Carex and its latitudinal pattern of species richness.
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Affiliation(s)
- Marcial Escudero
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA.
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Kuznetsova VG, Grozeva SM, Nokkala S, Nokkala C. Cytogenetics of the true bug infraorder Cimicomorpha (Hemiptera, Heteroptera): a review. Zookeys 2011; 154:31-70. [PMID: 22287915 PMCID: PMC3238039 DOI: 10.3897/zookeys.154.1953] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022] Open
Abstract
The Cimicomorpha is one of the largest and highly diversified infraorders of the Heteroptera. This group is also highly diversified cytogenetically and demonstrates a number of unusual cytogenetic characters such as holokinetic chromosomes; m-chromosomes; multiple sex chromosome systems; post-reduction of sex chromosomes in meiosis; variation in the presence/absence of chiasmata in spermatogenesis; different types of achiasmate meiosis. We present here a review of essential cytogenetic characters of the Cimicomorpha and outline the chief objectives and goals of future investigations in the field.
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Affiliation(s)
| | - Snejana M. Grozeva
- Institute of Biodiversity and Ecosystem research, BAS, Tsar Osvoboditel blvd, 1, Sofia 1000, Bulgaria
| | - Seppo Nokkala
- Laboratory of Genetics, Department of Biology, University of Turku, 20500 Turku, Finland
| | - Christina Nokkala
- Laboratory of Genetics, Department of Biology, University of Turku, 20500 Turku, Finland
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Jiménez-Mejías P, Escudero M, Guerra-Cárdenas S, Lye KA, Luceño M. Taxonomic delimitation and drivers of speciation in the Ibero-North African Carex sect. Phacocystis river-shore group (Cyperaceae). AMERICAN JOURNAL OF BOTANY 2011; 98:1855-1867. [PMID: 22025295 DOI: 10.3732/ajb.1100120] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The Ibero-North African Carex sect. Phacocystis river-shore group is a set of perennial helophytic species with poorly defined taxonomic boundaries. In the present study, we delimited the different taxonomic units, addressed the phylogeographic history, and evaluated the drivers of differentiation that have promoted diversification of these plants. METHODS We analyzed molecular data using statistical parsimony for plastid sequences (26 samples from 26 populations) and principal coordinate analysis, neighbor joining, and Bayesian analysis of population structure for AFLPs (186 samples from 26 populations). Chromosome numbers from 14 samples (9 populations) are newly reported. KEY RESULTS Three species can be distinguished (C. acuta, C. elata, and C. reuteriana). Unexpectedly for rhizome-growing helophytes, the vegetative reproduction detected was incidental. The widespread C. elata was found to be a genetically poorly differentiated taxon, whereas the local C. reuteriana displayed geographical structuring. Geographical factors seem to be the main driver of differentiation for both taxa. CONCLUSIONS Despite apparent morphological and ecological similarities, C. elata and C. reuteriana have disparate genetic structures and evolutionary histories, which may have originated from small ecological differences. Carex elata is broadly distributed throughout Europe, and its northern populations were recently founded, probably after the last glacial maximum. In contrast, C. reuteriana is an Ibero-North African endemic, with long-standing populations affected by isolation and limited gene flow. It is likely that high-density blocking effects and different gene-flow barriers act together to delimit its distribution and promote its relatively high population differentiation.
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Affiliation(s)
- Pedro Jiménez-Mejías
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, carretera de Utrera km 1, 41013 Seville, Spain.
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Lukhtanov VA, Dincă V, Talavera G, Vila R. Unprecedented within-species chromosome number cline in the Wood White butterfly Leptidea sinapis and its significance for karyotype evolution and speciation. BMC Evol Biol 2011; 11:109. [PMID: 21507222 PMCID: PMC3113740 DOI: 10.1186/1471-2148-11-109] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/20/2011] [Indexed: 01/16/2023] Open
Abstract
Background Species generally have a fixed number of chromosomes in the cell nuclei while between-species differences are common and often pronounced. These differences could have evolved through multiple speciation events, each involving the fixation of a single chromosomal rearrangement. Alternatively, marked changes in the karyotype may be the consequence of within-species accumulation of multiple chromosomal fissions/fusions, resulting in highly polymorphic systems with the subsequent extinction of intermediate karyomorphs. Although this mechanism of chromosome number evolution is possible in theory, it has not been well documented. Results We present the discovery of exceptional intraspecific variability in the karyotype of the widespread Eurasian butterfly Leptidea sinapis. We show that within this species the diploid chromosome number gradually decreases from 2n = 106 in Spain to 2n = 56 in eastern Kazakhstan, resulting in a 6000 km-wide cline that originated recently (8,500 to 31,000 years ago). Remarkably, intrapopulational chromosome number polymorphism exists, the chromosome number range overlaps between some populations separated by hundreds of kilometers, and chromosomal heterozygotes are abundant. We demonstrate that this karyotypic variability is intraspecific because in L. sinapis a broad geographical distribution is coupled with a homogenous morphological and genetic structure. Conclusions The discovered system represents the first clearly documented case of explosive chromosome number evolution through intraspecific and intrapopulation accumulation of multiple chromosomal changes. Leptidea sinapis may be used as a model system for studying speciation by means of chromosomally-based suppressed recombination mechanisms, as well as clinal speciation, a process that is theoretically possible but difficult to document. The discovered cline seems to represent a narrow time-window of the very first steps of species formation linked to multiple chromosomal changes that have occurred explosively. This case offers a rare opportunity to study this process before drift, dispersal, selection, extinction and speciation erase the traces of microevolutionary events and just leave the final picture of a pronounced interspecific chromosomal difference.
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Affiliation(s)
- Vladimir A Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Science, Petersburg, Russia.
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Chung KS, Weber JA, Hipp AL. Dynamics of chromosome number and genome size variation in a cytogenetically variable sedge (Carex scoparia var. scoparia, Cyperaceae). AMERICAN JOURNAL OF BOTANY 2011; 98:122-129. [PMID: 21613090 DOI: 10.3732/ajb.1000046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY High intraspecific cytogenetic variation in the sedge genus Carex (Cyperaceae) is hypothesized to be due to the "diffuse" or non-localized centromeres, which facilitate chromosome fission and fusion. If chromosome number changes are dominated by fission and fusion, then chromosome evolution will result primarily in changes in the potential for recombination among populations. Chromosome duplications, on the other hand, entail consequent opportunities for divergent evolution of paralogs. In this study, we evaluate whether genome size and chromosome number covary within species. METHODS We used flow cytometry to estimate genome sizes in Carex scoparia var. scoparia, sampling 99 plants (23 populations) in the Chicago region, and we used meiotic chromosome observations to document chromosome numbers and chromosome pairing relations. KEY RESULTS Chromosome numbers range from 2n = 62 to 2n = 68, and nuclear DNA 1C content from 0.342 to 0.361 pg DNA. Regressions of DNA content on chromosome number are nonsignificant for data analyzed by individual or population, and a regression model that excludes slope is favored over a model in which chromosome number predicts genome size. CONCLUSIONS Chromosome rearrangements within cytogenetically variable Carex species are more likely a consequence of fission and fusion than of duplication and deletion. Moreover, neither genome size nor chromosome number is spatially autocorrelated, which suggests the potential for rapid chromosome evolution by fission and fusion at a relatively fine geographic scale (<350 km). These findings have important implications for ecological restoration and speciation within the largest angiosperm genus of the temperate zone.
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Affiliation(s)
- Kyong-Sook Chung
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA
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Hipp AL, Rothrock PE, Whitkus R, Weber JA. Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes. Mol Ecol 2010; 19:3124-38. [PMID: 20618902 DOI: 10.1111/j.1365-294x.2010.04741.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes--chromosomes in which centromeric activity is distributed along the length of the chromosome--have not. We collected chromosome number and molecular genetic data in Carex scoparia, an eastern North American plant species with holocentric chromosomes and highly variable karyotype (2n = 56-70). There are no deep genetic breaks within C. scoparia that would suggest cryptic species differentiation. However, genetic distance between individuals is positively correlated with chromosome number difference and geographic distance. A positive correlation is also found between chromosome number and genetic distance in the western North American C. pachystachya (2n = 74-81). These findings suggest that geographic distance and the number of karyotype rearrangements separating populations affect the rate of gene flow between those populations. This is the first study to quantify the effects of holocentric chromosome rearrangements on the partitioning of intraspecific genetic variance.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL 60532-1293, USA.
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Selective microspore abortion correlated with aneuploidy: an indication of meiotic drive. ACTA ACUST UNITED AC 2010; 24:1-8. [DOI: 10.1007/s00497-010-0150-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/18/2010] [Indexed: 11/27/2022]
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Escudero M, Hipp AL, Luceño M. Karyotype stability and predictors of chromosome number variation in sedges: a study in Carex section Spirostachyae (Cyperaceae). Mol Phylogenet Evol 2010; 57:353-63. [PMID: 20655386 DOI: 10.1016/j.ympev.2010.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 07/19/2010] [Indexed: 11/25/2022]
Abstract
Previous work on holocentric chromosomes in the angiosperm genus Carex demonstrates that many of the traditional sections are marked by different ranges of chromosome number, suggesting phylogenetic autocorrelation. It has been hypothesized that shifting constraints on chromosome rearrangements may limit the potential for hybridization among lineages, promoting speciation. In this study, we evaluated alternative evolutionary models to test for such transitions in Carex section Spirostachyae as well as the relative effects of several plausible drivers of intraspecific chromosome diversity. Chromosome number variation in section Spirostachyae shows significant phylogenetic signal, but no evidence of clade-specific shifts in chromosome number distribution. This gradual model of chromosome evolution contrasts with the shifting equilibrium model previously identified in a younger section of the same genus, suggesting that section Spirostachyae may have a more slowly evolving karyotype. Chromosome number variance, on the other hand, exhibits low phylogenetic signal. Average time of coalescence rather than geographic range or chromosome number itself predicts chromosome number variance, demonstrating a previously unreported relationship between population history and cytogenetic variation.
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Affiliation(s)
- Marcial Escudero
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain.
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Abstract
Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size) between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small ( pg), there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.
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Mayrose I, Barker MS, Otto SP. Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy. Syst Biol 2009; 59:132-44. [PMID: 20525626 DOI: 10.1093/sysbio/syp083] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Itay Mayrose
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Michael S. Barker
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Sarah P. Otto
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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