1
|
Li Y, Ning Y, Zheng YC, Lou XY, Pan Z, Dong SB. Chromosome-Scale Genome Assembly for Soft-Stem Bulrush (Schoenoplectus tabernaemontani) Confirms a Clade-Specific Whole-Genome Duplication in Cyperaceae. Genome Biol Evol 2024; 16:evae141. [PMID: 38946297 PMCID: PMC11251425 DOI: 10.1093/gbe/evae141] [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: 03/18/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024] Open
Abstract
Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential in decontamination applications and carbon sequestration. Previous studies have shown that this species may have experienced recent polyploidization. This would make S. tabernaemontani a unique model to study the processes and consequences of whole-genome duplications in the context of the well-documented holocentric chromosomes and dysploidy events in Cyperaceae. However, the inference was not completely solid because it lacked homology information that is essential to ascertain polyploidy. We present here the first chromosome-level genome assembly for S. tabernaemontani. By combining Oxford Nanopore Technologies (ONT) long reads and Illumina short reads, plus chromatin conformation via the Hi-C method, we assembled a genome spanning 507.96 Mb, with 99.43% of Hi-C data accurately mapped to the assembly. The assembly contig N50 value was 3.62 Mb. The overall BUSCO score was 94.40%. About 68.94% of the genome was comprised of repetitive elements. A total of 36,994 protein-coding genes were predicted and annotated. Long terminal repeat retrotransposons accounted for ∼26.99% of the genome, surpassing the content observed in most sequenced Cyperid genomes. Our well-supported haploid assembly comprised 21 pseudochromosomes, each harboring putative holocentric centromeres. Our findings corroborated a karyotype of 2n = 2X = 42. We also confirmed a recent whole-genome duplication occurring after the divergence between Schoenoplecteae and Bolboschoeneae. Our genome assembly expands the scope of sequenced genomes within the Cyperaceae family, encompassing the fifth genus. It also provides research resources on Cyperid evolution and wetland conservation.
Collapse
Affiliation(s)
- Yang Li
- Huzhou University, Huzhou, China
| | - Yu Ning
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Prefecture of Aba, China
| | - Yan Chao Zheng
- East China Inventory and Planning Institute, Hangzhou, China
| | | | - Zhe Pan
- Sichuan Academy of Environmental Policy and Planning, Chengdu, China
| | - Shu Bin Dong
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| |
Collapse
|
2
|
Escudero M, Arroyo JM, Sánchez-Ramírez S, Jordano P. Founder events and subsequent genetic bottlenecks underlie karyotype evolution in the Ibero-North African endemic Carex helodes. ANNALS OF BOTANY 2024; 133:871-882. [PMID: 37400416 PMCID: PMC11082475 DOI: 10.1093/aob/mcad087] [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: 05/19/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND AND AIMS Despite chromosomal evolution being one of the major drivers of diversification in plants, we do not yet have a clear view of how new chromosome rearrangements become fixed within populations, which is a crucial step forward for understanding chromosomal speciation. METHODS In this study, we test the role of genetic drift in the establishment of new chromosomal variants in the context of hybrid dysfunction models of chromosomal speciation. We genotyped 178 individuals from seven populations (plus 25 seeds from one population) across the geographical range of Carex helodes (Cyperaceae). We also characterized karyotype geographical patterns of the species across its distribution range. For one of the populations, we performed a detailed study of the fine-scale, local spatial distribution of its individuals and their genotypes and karyotypes. KEY RESULTS Synergistically, phylogeographical and karyotypic evidence revealed two main genetic groups: southwestern Iberian Peninsula vs. northwestern African populations; and within Europe our results suggest a west-to-east expansion with signals of genetic bottlenecks. Additionally, we inferred a pattern of descending dysploidy, plausibly as a result of a west-to-east process of post-glacial colonization in Europe. CONCLUSIONS Our results give experimental support to the role of geographical isolation, drift and inbreeding in the establishment of new karyotypes, which is key in the speciation models of hybrid dysfunction.
Collapse
Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, 41012 Seville, Spain
- Department of Integrative Ecology, Doñana Biological Station, CSIC, 41092 Seville, Spain
| | - Juan Miguel Arroyo
- Department of Integrative Ecology, Doñana Biological Station, CSIC, 41092 Seville, Spain
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, M5S 3B2 Toronto, Ontario, Canada
| | - Pedro Jordano
- Department of Plant Biology and Ecology, University of Seville, 41012 Seville, Spain
- Department of Integrative Ecology, Doñana Biological Station, CSIC, 41092 Seville, Spain
| |
Collapse
|
3
|
Escudero M, Marques A, Lucek K, Hipp AL. Genomic hotspots of chromosome rearrangements explain conserved synteny despite high rates of chromosome evolution in a holocentric lineage. Mol Ecol 2023. [PMID: 37486041 DOI: 10.1111/mec.17086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosome rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for the extraordinary rates of chromosome evolution that many holocentric lineages exhibit. Long blocks of genome synteny have been reported in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Nothing is known from plants, however, despite the fact that holocentricity appears to have played a key role in the diversification of one of the largest angiosperm genera, Carex (Cyperaceae). In the current study, we compared genomes of Carex species and a distantly related Cyperaceae species to characterize conserved and rearranged genome regions. Our analyses span divergence times ranging between 2 and 50 million years. We also compared a C. scoparia chromosome-level genome assembly with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found longer genome synteny blocks than expected under a null model of random rearrangement breakpoints, even between very distantly related species. We also found repetitive DNA to be non-randomly associated with holocentromeres and rearranged regions of the genome. The evidence of conserved synteny in sedges despite high rates of chromosome fission and fusion suggests that conserved genomic hotspots of chromosome evolution related to repetitive DNA shape the evolution of recombination, gene order and crossability in sedges. This finding may help explain why sedges are able to maintain species cohesion even in the face of high interspecific chromosome rearrangements.
Collapse
Affiliation(s)
- Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Sevilla, Spain
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kay Lucek
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | | |
Collapse
|
4
|
Elliott TL, Zedek F, Barrett RL, Bruhl JJ, Escudero M, Hroudová Z, Joly S, Larridon I, Luceño M, Márquez-Corro JI, Martín-Bravo S, Muasya AM, Šmarda P, Thomas WW, Wilson KL, Bureš P. Chromosome size matters: genome evolution in the cyperid clade. ANNALS OF BOTANY 2022; 130:999-1014. [PMID: 36342743 PMCID: PMC9851305 DOI: 10.1093/aob/mcac136] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/03/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.
Collapse
Affiliation(s)
- Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Australian Botanic Garden, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes 6, 41012 Seville, Spain
| | - Zdenka Hroudová
- Institute of Botany of the Czech Academy of Sciences, 252 43 Průhonice, Czech Republic
- National Museum, Department of Botany, Cirkusová 1740, 193 00 Prague 9, Czech Republic
| | - Simon Joly
- Montreal Botanical Garden, 4101, Sherbrooke East, Montreal, QC H1X 2B2, Canada
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, 4101, Sherbrooke East, Montreal, QC H1X 2B2, Canada
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Modesto Luceño
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - José Ignacio Márquez-Corro
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km. 1, 41013, Seville, Spain
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africaand
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | | | - Karen L Wilson
- National Herbarium of New South Wales, Australian Institute of Botanical Science, Australian Botanic Garden, Locked Bag 6002, Mount Annan, New South Wales 2567, Australia
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| |
Collapse
|
5
|
Afonso Neto PC, Micolino R, Cardoso DC, Cristiano MP. Phylogenetic Reconstruction of the Ancestral Chromosome Number of the Genera Anochetus Mayr, 1861 and Odontomachus Latreille, 1804 (Hymenoptera: Formicidae: Ponerinae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.829989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent phylogenetic and molecular data are changing our knowledge about the relations between species and evolutionary processes resulting in the chromosome variation observed in ants (Hymenoptera: Formicidae). Ants exhibit remarkable variations in morphology, behavior, karyotypes, and chromosome structure. By assembling genetic and chromosome information about the trap-jaw ants from the subfamily Ponerinae, we reconstructed the phylogenetic relationships that inferred the monophyletic condition between the Anochetus and Odontomachus genera and estimated their ancestral haploid chromosome number. According to our inferences, these clades have an ancestral haploid chromosome number n = 15. The most recent common ancestor of Anochetus and Odontomachus has arisen between the Early Paleocene and the Early Eocene periods (time of the most recent common ancestor). In the Anochetus genus, we observed maintenance of the ancestral chromosome number estimated here in most species. This also suggests that pericentric inversions were the primary chromosomal rearrangement modulating the karyotype evolution of this genus. However, a reduction from n = 15–14 is observed in Anochetus emarginatus and Anochetus cf. madaraszi, which likely occurred by centromeric fusion. In contrast, the increase from the ancestral karyotype number in Anochetus horridus suggested centromeric fissions. Odontomachus showed maintenance of the ancestral chromosome number in the “rixosus group” and several gains in all species from the “haematodus group.” Our findings suggest that centromeric fissions and pericentric rearrangements lead to chromosomal changes in trap-jaw ants. Considering the ancestral state estimated here, changes in chromosome morphology are likely due to pericentric inversions, and chromosome number increases are likely due to centric fissions. The higher number of acrocentric or telocentric chromosomes in the karyotypes with n < 15 haploid chromosomes supports such an idea.
Collapse
|
6
|
Moen DS, Cabrera-Guzmán E, Caviedes-Solis IW, González-Bernal E, Hanna AR. Phylogenetic analysis of adaptation in comparative physiology and biomechanics: overview and a case study of thermal physiology in treefrogs. J Exp Biol 2022; 225:274250. [PMID: 35119071 DOI: 10.1242/jeb.243292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022]
Abstract
Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require data collection from many species, a challenge when this is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework - the Ornstein-Uhlenbeck process - that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold tolerance and characterized thermal performance curves in jumping for 12 species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our study shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.
Collapse
Affiliation(s)
- Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Elisa Cabrera-Guzmán
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Itzue W Caviedes-Solis
- Science Unit, Lingnan University, Hong Kong S.A.R., China.,Department of Biology, University of Washington, Seattle, WA 98105, USA
| | - Edna González-Bernal
- CONACYT - CIIDIR Oaxaca, Instituto Politécnico Nacional, Santa Cruz Xoxocotlán, C.P. 71230, Oaxaca, México
| | - Allison R Hanna
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| |
Collapse
|
7
|
Carta A, Bedini G, Peruzzi L. A deep dive into the ancestral chromosome number and genome size of flowering plants. THE NEW PHYTOLOGIST 2020; 228:1097-1106. [PMID: 32421860 DOI: 10.1111/nph.16668] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 05/22/2023]
Abstract
Chromosome number and genome variation in flowering plants have stimulated growing speculation about the ancestral chromosome number of angiosperms, but estimates so far remain equivocal. We used a probabilistic approach to model haploid chromosome number (n) changes along a phylogeny embracing more than 10 000 taxa, to reconstruct the ancestral chromosome number of the common ancestor of extant angiosperms and the most recent common ancestor for single angiosperm families. Independently, we carried out an analysis of 1C genome size evolution, including over 5000 taxa. Our analyses revealed an ancestral haploid chromosome number for angiosperms of n = 7, a diploid status, and an ancestral 1C of 1.73 pg. For 160 families, inferred ancestral n are provided for the first time. Both descending dysploidy and polyploidy played crucial roles in chromosome number evolution. While descending dysploidy is equally distributed early and late across the phylogeny, polyploidy is detected mainly towards the tips. Similarly, 1C genome size also increases (or decreases) significantly in late-branching lineages. Therefore, no evidence exists of a clear link between ancestral chromosome numbers and ancient polyploidization events, suggesting that further insights are needed to elucidate the organization of genome packaging into chromosomes.
Collapse
Affiliation(s)
- Angelino Carta
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Gianni Bedini
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| | - Lorenzo Peruzzi
- Department of Biology, Botany Unit, University of Pisa, via Derna 1, Pisa, I-56126, Italy
| |
Collapse
|
8
|
Ruckman SN, Jonika MM, Casola C, Blackmon H. Chromosome number evolves at equal rates in holocentric and monocentric clades. PLoS Genet 2020; 16:e1009076. [PMID: 33048946 PMCID: PMC7584213 DOI: 10.1371/journal.pgen.1009076] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/23/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Despite the fundamental role of centromeres two different types are observed across plants and animals. Monocentric chromosomes possess a single region that function as the centromere while in holocentric chromosomes centromere activity is spread across the entire chromosome. Proper segregation may fail in species with monocentric chromosomes after a fusion or fission, which may lead to chromosomes with no centromere or multiple centromeres. In contrast, species with holocentric chromosomes should still be able to safely segregate chromosomes after fusion or fission. This along with the observation of high chromosome number in some holocentric clades has led to the hypothesis that holocentricity leads to higher rates of chromosome number evolution. To test for differences in rates of chromosome number evolution between these systems, we analyzed data from 4,393 species of insects in a phylogenetic framework. We found that insect orders exhibit striking differences in rates of fissions, fusions, and polyploidy. However, across all insects we found no evidence that holocentric clades have higher rates of fissions, fusions, or polyploidy than monocentric clades. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes. Instead, we suggest that other co-evolving traits must explain striking differences between clades.
Collapse
Affiliation(s)
- Sarah N. Ruckman
- Department of Biology, Texas A&M University, Texas, United States of America
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, Texas, United States of America
| | - Michelle M. Jonika
- Department of Biology, Texas A&M University, Texas, United States of America
- Genetics Interdisciplinary Program, Texas A&M University, Texas, United States of America
| | - Claudio Casola
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, Texas, United States of America
- Genetics Interdisciplinary Program, Texas A&M University, Texas, United States of America
- Department of Ecology and Conservation Biology, Texas A&M, Texas, United States of America
| | - Heath Blackmon
- Department of Biology, Texas A&M University, Texas, United States of America
- Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, Texas, United States of America
- Genetics Interdisciplinary Program, Texas A&M University, Texas, United States of America
- * E-mail:
| |
Collapse
|
9
|
Fuentes-G JA, Polly PD, Martins EP. A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates. Evolution 2019; 74:311-325. [PMID: 31849034 DOI: 10.1111/evo.13899] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/01/2022]
Abstract
Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.
Collapse
Affiliation(s)
- Jesualdo A Fuentes-G
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
| | - Paul David Polly
- Department of Earth and Atmospheric Sciences, Indiana University, Bloomington, Indiana
| | - Emília P Martins
- School of Life Sciences, Arizona State University, Tempe, Arizona
| |
Collapse
|
10
|
Schwarzer C, Joshi J. Ecotypic differentiation, hybridization and clonality facilitate the persistence of a cold-adapted sedge in European bogs. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Recent research has shown that many cold-adapted species survived the last glacial maximum (LGM) in northern refugia. Whether this evolutionary history has had consequences for their genetic diversity and adaptive potential remains unknown. We sampled 14 populations of Carex limosa, a sedge specialized to bog ecosystems, along a latitudinal gradient from its Scandinavian core to the southern lowland range-margin in Germany. Using microsatellite and experimental common-garden data, we evaluated the impacts of global climate change along this gradient and assessed the conservation status of the southern marginal populations. Microsatellite data revealed two highly distinct genetic groups and hybrid individuals. In our common-garden experiment, the two groups showed divergent responses to increased nitrogen/phosphorus (N/P) availability, suggesting ecotypic differentiation. Each group formed genetically uniform populations at both northern and southern sampling areas. Mixed populations occurred throughout our sampling area, an area that was entirely glaciated during the LGM. The fragmented distribution implies allopatric divergence at geographically separated refugia that putatively differed in N/P availability. Molecular data and an observed low hybrid fecundity indicate the importance of clonal reproduction for hybrid populations. At the southern range-margin, however, all populations showed effects of clonality, lowered fecundity and low competitiveness, suggesting abiotic and biotic constraints to population persistence.
Collapse
Affiliation(s)
- Christian Schwarzer
- University of Potsdam, Biodiversity Research/Systematic Botany, Maulbeerallee 1, 14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
| | - Jasmin Joshi
- University of Potsdam, Biodiversity Research/Systematic Botany, Maulbeerallee 1, 14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 6, 14195 Berlin, Germany
- Hochschule für Technik HSR Rapperswil, Institute for Landscape and Open Space, Oberseestrasse 10, 8640 Rapperswil, Switzerland
| |
Collapse
|
11
|
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]
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Stapley J, Feulner PGD, Johnston SE, Santure AW, Smadja CM. Variation in recombination frequency and distribution across eukaryotes: patterns and processes. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0455. [PMID: 29109219 PMCID: PMC5698618 DOI: 10.1098/rstb.2016.0455] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 01/04/2023] Open
Abstract
Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
Collapse
Affiliation(s)
- Jessica Stapley
- Centre for Adaptation to a Changing Environment, IBZ, ETH Zürich, 8092 Zürich, Switzerland
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JY, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Carole M Smadja
- Institut des Sciences de l'Evolution UMR 5554, CNRS, IRD, EPHE, Université de Montpellier, 3095 Montpellier cedex 05, France
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Toljagic O, Voje KL, Matschiner M, Liow LH, Hansen TF. Millions of Years Behind: Slow Adaptation of Ruminants to Grasslands. Syst Biol 2018. [PMID: 28637223 DOI: 10.1093/sysbio/syx059] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Late Cretaceous appearance of grasses, followed by the Cenozoic advancement of grasslands as dominant biomes, has contributed to the evolution of a range of specialized herbivores adapted to new diets, as well as to increasingly open and arid habitats. Many mammals including ruminants, the most diversified ungulate suborder, evolved high-crowned (hypsodont) teeth as an adaptation to tooth-wearing diets and habitats. The impact of different causes of tooth wear is still a matter of debate, and the temporal pattern of hypsodonty evolution in relation to the evolution of grasslands remains unclear. We present an improved time-calibrated molecular phylogeny of Cetartiodactyla, with phylogenetic reconstruction of ancestral ruminant diets and habitats, based on characteristics of extant taxa. Using this timeline, as well as the fossil record of grasslands, we conduct phylogenetic comparative analyses showing that hypsodonty in ruminants evolved as an adaptation to both diet and habitat. Our results demonstrate a slow, perhaps constrained, evolution of hypsodonty toward estimated optimal states, excluding the possibility of immediate adaptation. This augments recent findings that slow adaptation is not uncommon on million-year time scales.
Collapse
Affiliation(s)
- Olja Toljagic
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Kjetil L Voje
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| | - Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway.,Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Lee Hsiang Liow
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway.,Natural History Museum, University of Oslo, Sars gate 1, NO-0562 Oslo, Norway
| | - Thomas F Hansen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, NO-0371 Oslo, Norway
| |
Collapse
|
16
|
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: 9] [Impact Index Per Article: 1.5] [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.
Collapse
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.
| |
Collapse
|
17
|
Léveillé-Bourret É, Starr JR, Ford BA. Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae). Mol Phylogenet Evol 2017; 119:93-104. [PMID: 29113924 DOI: 10.1016/j.ympev.2017.10.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers. Ancestral state reconstructions of key characters were made, and a time-calibrated tree estimated. Carex is strongly supported as sister to the rare East Asian Sumatroscirpus, sole genus of a new tribe, Sumatroscirpeae trib. nov. Believed to be unique to Carex, the perigynium (prophyllar bract enclosing a flower) is in fact a synapomorphy shared with this small tribe (∼4 species) that appeared 36 Mya. We thus suggest the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints on perigynia through spikelet truncation, resulting in novel adaptive morphologies. Monoecy, chromosomal change, and rapid inflorescence development enabling phenological isolation may also be involved. The tiny tribe Sumatroscirpeae will provide unprecedented insights into the inflorescence homology, evolution, diversification, and biogeographic history of its sister-group Carex, one of the world's most diverse plant lineages.
Collapse
Affiliation(s)
| | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Bruce A Ford
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| |
Collapse
|
18
|
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.
Collapse
|
19
|
Veleba A, Šmarda P, Zedek F, Horová L, Šmerda J, Bureš P. Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae). ANNALS OF BOTANY 2017; 119:409-416. [PMID: 28025291 PMCID: PMC5314647 DOI: 10.1093/aob/mcw229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.
Collapse
Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ 61137, Czech Republic
| |
Collapse
|
20
|
Fuentes-G. JA, Housworth EA, Weber A, Martins EP. Phylogenetic ANCOVA: Estimating Changes in Evolutionary Rates as Well as Relationships between Traits. Am Nat 2016; 188:615-627. [DOI: 10.1086/688917] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
21
|
Abrahamczyk S, Kessler M, Hanley D, Karger DN, Müller MPJ, Knauer AC, Keller F, Schwerdtfeger M, Humphreys AM. Pollinator adaptation and the evolution of floral nectar sugar composition. J Evol Biol 2016; 30:112-127. [PMID: 27747987 DOI: 10.1111/jeb.12991] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 12/30/2022]
Abstract
A long-standing debate concerns whether nectar sugar composition evolves as an adaptation to pollinator dietary requirements or whether it is 'phylogenetically constrained'. Here, we use a modelling approach to evaluate the hypothesis that nectar sucrose proportion (NSP) is an adaptation to pollinators. We analyse ~ 2100 species of asterids, spanning several plant families and pollinator groups (PGs), and show that the hypothesis of adaptation cannot be rejected: NSP evolves towards two optimal values, high NSP for specialist-pollinated and low NSP for generalist-pollinated plants. However, the inferred adaptive process is weak, suggesting that adaptation to PG only provides a partial explanation for how nectar evolves. Additional factors are therefore needed to fully explain nectar evolution, and we suggest that future studies might incorporate floral shape and size and the abiotic environment into the analytical framework. Further, we show that NSP and PG evolution are correlated - in a manner dictated by pollinator behaviour. This contrasts with the view that a plant necessarily has to adapt its nectar composition to ensure pollination but rather suggests that pollinators adapt their foraging behaviour or dietary requirements to the nectar sugar composition presented by the plants. Finally, we document unexpectedly sucrose-poor nectar in some specialized nectarivorous bird-pollinated plants from the Old World, which might represent an overlooked form of pollinator deception. Thus, our broad study provides several new insights into how nectar evolves and we conclude by discussing why maintaining the conceptual dichotomy between adaptation and constraint might be unhelpful for advancing this field.
Collapse
Affiliation(s)
- S Abrahamczyk
- Nees Institute for Plant Biodiversity, University of Bonn, Bonn, Germany
| | - M Kessler
- Institute of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - D Hanley
- Department of Biology, Long Island University - Post, Brookville, NY, USA
| | - D N Karger
- Institute of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - M P J Müller
- Institute of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - A C Knauer
- Institute of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - F Keller
- Institute of Plant Science, University of Zurich, Zurich, Switzerland
| | - M Schwerdtfeger
- Albrecht-v.-Haller Institute of Plant Science, University of Goettingen, Goettingen, Germany
| | - A M Humphreys
- Department of Life Sciences, Imperial College London, Berkshire, UK.,Department of Ecology, Environment and Plant Sciences, University of Stockholm, Stockholm, Sweden
| |
Collapse
|
22
|
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: 22] [Impact Index Per Article: 2.8] [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.
Collapse
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
| |
Collapse
|
23
|
Zedek F, Veselý P, Horová L, Bureš P. Flow cytometry may allow microscope-independent detection of holocentric chromosomes in plants. Sci Rep 2016; 6:27161. [PMID: 27255216 PMCID: PMC4891681 DOI: 10.1038/srep27161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/13/2016] [Indexed: 01/03/2023] Open
Abstract
Two chromosomal structures, known as monocentric and holocentric chromosomes, have evolved in eukaryotes. Acentric fragments of monocentric chromosomes are unequally distributed to daughter cells and/or lost, while holocentric fragments are inherited normally. In monocentric species, unequal distribution should generate chimeras of cells with different nuclear DNA content. We investigated whether such differences in monocentric species are detectable by flow cytometry (FCM) as (i) a decreased nuclear DNA content and (ii) an increased coefficient of variance (CV) of the G1 peak after gamma radiation-induced fragmentation. We compared 13 monocentric and 9 holocentric plant species. Unexpectedly, monocentrics and holocentrics did not differ with respect to parameters (i) and (ii) in their response to gamma irradiation. However, we found that the proportion of G2 nuclei was highly elevated in monocentrics after irradiation, while holocentrics were negligibly affected. Therefore, we hypothesize that DNA-damaging agents induce cell cycle arrest leading to endopolyploidy only in monocentric and not (or to much lesser extent) in holocentric plants. While current microscope-dependent methods for holocentrism detection are unreliable for small and numerous chromosomes, which are common in holocentrics, FCM can use somatic nuclei. Thus, FCM may be a rapid and reliable method of high-throughput screening for holocentric candidates across plant phylogeny.
Collapse
Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| |
Collapse
|
24
|
Starr JR, Janzen FH, Ford BA. Three new, early diverging Carex (Cariceae, Cyperaceae) lineages from East and Southeast Asia with important evolutionary and biogeographic implications. Mol Phylogenet Evol 2015; 88:105-20. [DOI: 10.1016/j.ympev.2015.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/26/2015] [Accepted: 04/01/2015] [Indexed: 12/25/2022]
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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]
|
27
|
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.
Collapse
Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | | |
Collapse
|
28
|
Escudero M, Hipp A. Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:2403-2411. [PMID: 24249788 DOI: 10.3732/ajb.1300162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
PREMISE OF THE STUDY Understanding heterogeneity in species richness across the tree of life is a challenge in evolutionary biology. The sedge family, Cyperaceae, is classified into tribes that exhibit a roughly 200-fold range in species richness. The Cyperaceae present an excellent case study in the determinants of species richness within higher-level taxa. METHODS We used secondary calibration based on prior studies and fossils from a rush (Juncaceae) and five sedges to calibrate two previously published Cyperaceae phylogenies, then compared our results to previous molecular clock analyses. We used an information-theoretic approach to identify shifts in lineage diversification rates and phylogenetic generalized least squares to fit alternative models of clade species richness. KEY RESULTS Our results suggest a late Cretaceous origin for Cyperaceae (76-89 mya). The inferred 0.06 speciation events Ma(-1) is comparable to overall diversification rates in the order Poales but faster than angiosperm background rates. A threefold increase in diversification rate at the base of the species-rich SDC+FAEC clade is correlated with climatic changes during the Paleocene-Eocene boundary (ca. 55 mya). The greater driver of among-clade variance in species richness, however, is clade age (simple R(2) = 0.334, P = 0.0006). CONCLUSIONS Although shifts in diversification rates play a role in the generation of heterogeneous patterns of species richness, our study demonstrates that variance in clade age alone explains ca. 33% of among-clade variation in species diversity, which stands in contrast to the general pattern for angiosperms.
Collapse
Affiliation(s)
- Marcial Escudero
- Department of Botany, The Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, Illinois 60605 USA
| | | |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Ellis THN, Moore G. Recombination, and chromosomes, in a changing environment. THE NEW PHYTOLOGIST 2012; 195:8-9. [PMID: 22626262 DOI: 10.1111/j.1469-8137.2012.04192.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- T H Noel Ellis
- IBERS, Gogerddan Campus, Aberystwyth University, Aberystwyth, Ceredigion, UK.
| | | |
Collapse
|