The Experts below are selected from a list of 216 Experts worldwide ranked by ideXlab platform
Lorenzo Peruzzi - One of the best experts on this subject based on the ideXlab platform.
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A deep dive into the ancestral Chromosome Number and genome size of flowering plants
The New phytologist, 2020Co-Authors: Angelino Carta, Gianni Bedini, Lorenzo PeruzziAbstract: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.
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A deep dive into the ancestral Chromosome Number and genome size of flowering plants
2020Co-Authors: Angelino Carta, Gianni Bedini, Lorenzo PeruzziAbstract:Chromosome Number and genome variation in flowering plants has stimulated a blossoming Number of speculations 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 thousands 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 5 thousands taxa. Our inferences revealed an ancestral haploid Chromosome Number for angiosperms n = 7, a diploid status, and an ancestral 1C = 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, also 1C genome size significantly increases (or decreases) in late-branching lineages. Therefore, no evidence exists for 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.
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Unscrambling phylogenetic effects and ecological determinants of Chromosome Number in major angiosperm clades.
Scientific reports, 2018Co-Authors: Angelino Carta, Gianni Bedini, Lorenzo PeruzziAbstract: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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Online resources for Chromosome Number databases
Caryologia, 2014Co-Authors: Lorenzo Peruzzi, Gianni BediniAbstract:Available online resources for animal and plant Chromosome Number databases are surveyed and briefly discussed.
Itay Mayrose - One of the best experts on this subject based on the ideXlab platform.
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Model adequacy tests for probabilistic models of Chromosome-Number evolution.
The New phytologist, 2021Co-Authors: Anna Rice, Itay MayroseAbstract:Chromosome Number is a central feature of eukaryote genomes. Deciphering patterns of Chromosome-Number change along a phylogeny is central to the inference of whole genome duplications and ancestral Chromosome Numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of Chromosome-Number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data. Here, we present a model adequacy test for likelihood models of Chromosome-Number evolution. The procedure allows us to determine whether the model can generate data with similar characteristics as those found in the observed ones. We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitting model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present. The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutionary patterns deviate substantially from current modelling assumptions and should guide future methods development.
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Probabilistic models of Chromosome Number evolution and the inference of polyploidy.
Systematic biology, 2009Co-Authors: Itay Mayrose, Michael S. Barker, Sarah P. OttoAbstract:Polyploidy, the genome wide duplication of Chromosome Number, is a key feature in eukaryote evolution. Poly- ploidy exists in diverse groups including animals, fungi, and invertebrates but is especially prevalent in plants with most, if not all, plant species having descended from a polyploidization event. Polyploids often differ markedly from their diploid progenitors in morphological, physiological, and life history characteristics as well as rates of adaptation. The altered char- acteristics displayed by polyploids may contribute to their success in novel ecological habitats. Clearly, a better understand- ing of the processes underlying changes in the Number of Chromosomes within genomes is a key goal in our understanding of speciation and adaptation for a wide range of families and genera. Despite the fundamental role of Chromosome Number change in eukaryotic evolution, probabilistic models describing the evolution of Chromosome Number along a phylogeny have not yet been formulated. We present a series of likelihood models, each representing a different hypothesis regarding the evolution of Chromosome Number along a given phylogeny. These models allow us to reconstruct ancestral Chromosome Numbers and to estimate the expected Number of polyploidization events and single Chromosome changes (dysploidy) that occurred along a phylogeny. We test, using simulations, the accuracy of this approach and its dependence on the Number of taxa and tree length. We then demonstrate the application of the method for the study of Chromosome Number evolution in 4 plant genera: Aristolochia, Carex, Passiflora , and Helianthus. Considering the depth of the available cytological and phy- logenetic data, formal models of Chromosome Number evolution are expected to advance significantly our understanding of the importance of polyploidy and dysploidy across different taxonomic groups. (Chromosome evolution; dysploidy; evolutionary models; genome duplication; polyploidy.)
Angelino Carta - One of the best experts on this subject based on the ideXlab platform.
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A deep dive into the ancestral Chromosome Number and genome size of flowering plants
The New phytologist, 2020Co-Authors: Angelino Carta, Gianni Bedini, Lorenzo PeruzziAbstract: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.
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A deep dive into the ancestral Chromosome Number and genome size of flowering plants
2020Co-Authors: Angelino Carta, Gianni Bedini, Lorenzo PeruzziAbstract:Chromosome Number and genome variation in flowering plants has stimulated a blossoming Number of speculations 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 thousands 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 5 thousands taxa. Our inferences revealed an ancestral haploid Chromosome Number for angiosperms n = 7, a diploid status, and an ancestral 1C = 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, also 1C genome size significantly increases (or decreases) in late-branching lineages. Therefore, no evidence exists for 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.
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Unscrambling phylogenetic effects and ecological determinants of Chromosome Number in major angiosperm clades.
Scientific reports, 2018Co-Authors: Angelino Carta, Gianni Bedini, Lorenzo PeruzziAbstract: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.
Sarah P. Otto - One of the best experts on this subject based on the ideXlab platform.
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Probabilistic models of Chromosome Number evolution and the inference of polyploidy.
Systematic biology, 2009Co-Authors: Itay Mayrose, Michael S. Barker, Sarah P. OttoAbstract:Polyploidy, the genome wide duplication of Chromosome Number, is a key feature in eukaryote evolution. Poly- ploidy exists in diverse groups including animals, fungi, and invertebrates but is especially prevalent in plants with most, if not all, plant species having descended from a polyploidization event. Polyploids often differ markedly from their diploid progenitors in morphological, physiological, and life history characteristics as well as rates of adaptation. The altered char- acteristics displayed by polyploids may contribute to their success in novel ecological habitats. Clearly, a better understand- ing of the processes underlying changes in the Number of Chromosomes within genomes is a key goal in our understanding of speciation and adaptation for a wide range of families and genera. Despite the fundamental role of Chromosome Number change in eukaryotic evolution, probabilistic models describing the evolution of Chromosome Number along a phylogeny have not yet been formulated. We present a series of likelihood models, each representing a different hypothesis regarding the evolution of Chromosome Number along a given phylogeny. These models allow us to reconstruct ancestral Chromosome Numbers and to estimate the expected Number of polyploidization events and single Chromosome changes (dysploidy) that occurred along a phylogeny. We test, using simulations, the accuracy of this approach and its dependence on the Number of taxa and tree length. We then demonstrate the application of the method for the study of Chromosome Number evolution in 4 plant genera: Aristolochia, Carex, Passiflora , and Helianthus. Considering the depth of the available cytological and phy- logenetic data, formal models of Chromosome Number evolution are expected to advance significantly our understanding of the importance of polyploidy and dysploidy across different taxonomic groups. (Chromosome evolution; dysploidy; evolutionary models; genome duplication; polyploidy.)
Yongping Yang - One of the best experts on this subject based on the ideXlab platform.
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Chromosome Number and genome size variation in colocasia araceae from china
Journal of Plant Research, 2017Co-Authors: Guangyan Wang, Xiaoming Zhang, Min Qian, Xiangyang Hu, Yongping YangAbstract:Chromosome Number and genome size are important cytological characters that significantly influence various organismal traits. We investigated Chromosome Number and genome size variation in 73 accessions belonging to four Colocasia species from China. Five different Chromosome counts (2n = 26, 28, 38, 42, and 56) were found, the largest one representing a new record in Colocasia. The basic Chromosome Numbers are x = 13, 14, and 19, corresponding to 2x, 3x, and 4x cytotypes. Yunnan Province, China is considered the center of Colocasia polyploid origin. The 2C values in our accessions ranged from 3.29 pg in C. gigantea to 12.51 pg in C. esculenta. All species exhibit inter- and intraspecific chromosomal variation. Differences in DNA content among the Colocasia species seem to have occurred by chromosomal gain under similar habitats. Polyploidization also obviously contributes to 2C value variation.