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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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2
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods. Animals (Basel) 2023; 13:ani13061033. [PMID: 36978574 PMCID: PMC10044425 DOI: 10.3390/ani13061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
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3
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Chaves ALA, Carvalho PHM, Ferreira MTM, Benites FRG, Techio VH. Genomic constitution, allopolyploidy, and evolutionary proposal for Cynodon Rich. based on GISH. PROTOPLASMA 2022; 259:999-1011. [PMID: 34709474 DOI: 10.1007/s00709-021-01716-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Polyploidy is the main mechanism for chromosome number variation in Cynodon. Taxonomic boundaries are difficult to define and, although phylogenetic studies indicate that some species are closely related, the degree of genomic similarity remains unknown. Furthermore, the Cynodon species classification as auto or allopolyploids is still controversial. Thus, this study aimed to investigate the genomic constitution in diploid and polyploid species using different approaches of genomic in situ hybridization (GISH). To better understand the hybridization events, we also investigated the occurrence of unreduced gametes in C. dactylon diploid pollen grains. We suggest a genomic nomenclature of diploid species as DD, D1D1, and D2D2 for C. dactylon, C. incompletus, and C. nlemfuensis, and DDD2D2 and DD2D1D1 for the segmental allotetraploids of Cynodon dactylon and C. transvaalensis, respectively. Furthermore, an evolutionary proposal was built based on our results and previous data from other studies, showing possible crosses that may have occurred between Cynodon species.
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Affiliation(s)
- Ana Luisa Arantes Chaves
- Department of Biology (DBI), Plant Cytogenetics Laboratory, Federal University of Lavras (UFLA), P.O. Box 3037, Lavras, Minas Gerais State, Brazil
| | - Pedro Henrique Mendes Carvalho
- Department of Biology (DBI), Plant Cytogenetics Laboratory, Federal University of Lavras (UFLA), P.O. Box 3037, Lavras, Minas Gerais State, Brazil
| | - Marco Tulio Mendes Ferreira
- Department of Biology (DBI), Plant Cytogenetics Laboratory, Federal University of Lavras (UFLA), P.O. Box 3037, Lavras, Minas Gerais State, Brazil
| | | | - Vânia Helena Techio
- Department of Biology (DBI), Plant Cytogenetics Laboratory, Federal University of Lavras (UFLA), P.O. Box 3037, Lavras, Minas Gerais State, Brazil.
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4
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Evans BJ, Upham NS, Golding GB, Ojeda RA, Ojeda AA. Evolution of the Largest Mammalian Genome. Genome Biol Evol 2018; 9:1711-1724. [PMID: 28854639 PMCID: PMC5569995 DOI: 10.1093/gbe/evx113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/31/2022] Open
Abstract
The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansion is controversial, and hypothesized to be a consequence of whole genome duplication or accumulation of repetitive elements. To test these alternative but nonexclusive hypotheses, we gathered and evaluated evidence from whole transcriptome and whole genome sequences of T. barrerae and O. mimax. We recovered support for genome expansion due to accumulation of a diverse assemblage of repetitive elements, which represent about one half and one fifth of the genomes of T. barrerae and O. mimax, respectively, but we found no strong signal of whole genome duplication. In both species, repetitive sequences were rare in transcribed regions as compared with the rest of the genome, and mostly had no close match to annotated repetitive sequences from other rodents. These findings raise new questions about the genomic dynamics of these repetitive elements, their connection to widespread chromosomal fissions that occurred in the T. barrerae ancestor, and their fitness effects—including during the evolution of hypersaline dietary tolerance in T. barrerae.
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Affiliation(s)
- Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Nathan S Upham
- Biology Department, McMaster University, Hamilton, Ontario, Canada.,Field Museum of Natural History, Chicago, IL.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | | | - Ricardo A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
| | - Agustina A Ojeda
- Grupo de Investigaciones de la Biodiversidad (GIB), Instituto Argentino de Investigaciones de Zonas Áridas (IADIZA), Mendoza, Argentina
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5
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MacKintosh C, Ferrier DEK. Recent advances in understanding the roles of whole genome duplications in evolution. F1000Res 2017; 6:1623. [PMID: 28928963 PMCID: PMC5590085 DOI: 10.12688/f1000research.11792.2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2018] [Indexed: 01/21/2023] Open
Abstract
Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.
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Affiliation(s)
- Carol MacKintosh
- Division of Cell and Developmental Biology, University of Dundee, Dundee, Scotland, DD1 5EH, UK
| | - David E K Ferrier
- The Scottish Oceans Institute, University of St Andrews, Scotland, KY16 8LB, UK
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7
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Filling phylogenetic gaps and the biogeographic relationships of the Octodontidae (Mammalia: Hystricognathi). Mol Phylogenet Evol 2016; 105:96-101. [DOI: 10.1016/j.ympev.2016.08.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 08/03/2016] [Accepted: 08/23/2016] [Indexed: 11/18/2022]
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Suárez-Villota EY, Haro RE, Vargas RA, Gallardo MH. The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials. Mol Cytogenet 2016; 9:59. [PMID: 27489568 PMCID: PMC4971695 DOI: 10.1186/s13039-016-0270-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/25/2016] [Indexed: 11/12/2022] Open
Abstract
Background The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials’ cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GISH) were used to detect telomeric and repetitive sequences, respectively. These were complemented with C-, fluorescent banding, and centromere immunodetection over mitotic spreads. The presence of interstitial telomeric sequences (ITS) and diploid numbers were reconstructed and mapped onto the marsupial phylogenetic tree. Results No interstitial, fluorescent signals, but clearly stained telomeric regions were detected by FISH and self-GISH. Heterochromatin distribution was sparse in the telomeric/subtelomeric regions of large submetacentric chromosomes. Large AT-rich blocks were detected in the long arm of four submetacentrics and CG-rich block in the telomeric regions of all chromosomes. The ancestral reconstructions both ITS presence and diploid numbers suggested that ITS are unrelated to fusion events. Conclusion Although the lack of interstitial signals in D. gliroides’ karyotype does not prove absence of past fusions, our data suggests its non-rearranged plesiomorphic condition. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0270-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elkin Y Suárez-Villota
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Ronie E Haro
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Rodrigo A Vargas
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Milton H Gallardo
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
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9
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Lukhtanov VA. The blue butterfly Polyommatus (Plebicula) atlanticus (Lepidoptera, Lycaenidae) holds the record of the highest number of chromosomes in the non-polyploid eukaryotic organisms. COMPARATIVE CYTOGENETICS 2015; 9:683-90. [PMID: 26753083 PMCID: PMC4698580 DOI: 10.3897/compcytogen.v9i4.5760] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 08/30/2014] [Indexed: 05/08/2023]
Abstract
The blue butterfly species Polyommatus (Plebicula) atlanticus (Elwes, 1906) (Lepidoptera, Lycaenidae) is known to have a very high haploid number of chromosomes (n= circa 223). However, this approximate count made by Hugo de Lesse 45 years ago was based on analysis of a single meiotic I metaphase plate, not confirmed by study of diploid chromosome set and not documented by microphotographs. Here I demonstrate that (1) Polyommatus atlanticus is a diploid (non-polyploid) species, (2) its meiotic I chromosome complement includes at least 224-226 countable chromosome bodies, and (3) all (or nearly all) chromosome elements in meiotic I karyotype are represented by bivalents. I also provide the first data on the diploid karyotype and estimate the diploid chromosome number as 2n=ca448-452. Thus, Polyommatus atlanticus is confirmed to possess the highest chromosome number among all the non-polyploid eukaryotic organisms.
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Affiliation(s)
- Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 St. Petersburg, Russia
- Department of Entomology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
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10
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Huang X, Bi K, Lu W, Wang S, Zhang L, Bao Z. Genomic in situ hybridization identifies parental chromosomes in hybrid scallop (Bivalvia, Pectinoida, Pectinidae) between female Chlamysfarreri and male Argopectenirradiansirradians. COMPARATIVE CYTOGENETICS 2015; 9:189-200. [PMID: 26140161 PMCID: PMC4488966 DOI: 10.3897/compcytogen.v9i2.8943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Interspecific crossing was artificially carried out between Chlamysfarreri (Jones & Preston, 1904) ♀ and Argopectenirradiansirradians (Lamarck, 1819) ♂, two of the dominant cultivated scallop species in China. Genomic in situ hybridization (GISH) was used to examine the chromosome constitution and variation in hybrids at early embryonic stage. The number of chromosomes in 66.38% of the metaphases was 2n = 35 and the karyotype was 2n = 3 m + 5 sm + 16 st + 11 t. After GISH, two parental genomes were clearly distinguished in hybrids, most of which comprised 19 chromosomes derived from their female parent (Chlamysfarreri) and 16 chromosomes from their male parent (Argopectenirradiansirradians). Some chromosome elimination and fragmentation was also observed in the hybrids.
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Affiliation(s)
- Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Ke Bi
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
| | - Wei Lu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Lingling Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
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Suárez-Villota EY, Pansonato-Alves JC, Foresti F, Gallardo MH. Homomorphic Sex Chromosomes and the Intriguing Y Chromosome of Ctenomys Rodent Species (Rodentia, Ctenomyidae). Cytogenet Genome Res 2014; 143:232-40. [DOI: 10.1159/000366173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 11/19/2022] Open
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12
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Teta P, Pardiñas UFJ, Sauthier DEU, Gallardo MH. A new species of the tetraploid vizcacha ratTympanoctomys(Caviomorpha, Octodontidae) from central Patagonia, Argentina. J Mammal 2014. [DOI: 10.1644/13-mamm-a-160] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Arkhipova IR, Rodriguez F. Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids. Cytogenet Genome Res 2013; 140:295-311. [PMID: 23899811 DOI: 10.1159/000352069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) are discrete genetic units that have the ability to change their location within chromosomal DNA, and constitute a major and rapidly evolving component of eukaryotic genomes. They can be subdivided into 2 distinct types: retrotransposons, which use an RNA intermediate for transposition, and DNA transposons, which move only as DNA. Rapid advances in genome sequencing significantly improved our understanding of TE roles in genome shaping and restructuring, and studies of transcriptomes and epigenomes shed light on the previously unknown molecular mechanisms underlying genetic and epigenetic TE controls. Knowledge of these control systems may be important for better understanding of reticulate evolution and speciation in the context of bringing different genomes together by hybridization and perturbing the established regulatory balance by ploidy changes. See also sister article focusing on plants by Bento et al. in this themed issue.
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Affiliation(s)
- I R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA. iarkhipova @ mbl.edu
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Wertheim B, Beukeboom L, van de Zande L. Polyploidy in Animals: Effects of Gene Expression on Sex Determination, Evolution and Ecology. Cytogenet Genome Res 2013; 140:256-69. [DOI: 10.1159/000351998] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Gallardo MH, Suárez-Villota EY, Nuñez JJ, Vargas RA, Haro R, Köhler N. Phylogenetic analysis and phylogeography of the tetraploid rodentTympanoctomys barrerae(Octodontidae): insights on its origin and the impact of Quaternary climate changes on population dynamics. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.02016.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Milton H. Gallardo
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | | | - José J. Nuñez
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | - Rodrigo A. Vargas
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | - Ronie Haro
- Institute of Marine and Limnological Sciences; Universidad Austral de Chile; Casilla 567; Valdivia; Chile
| | - Nélida Köhler
- Institute of Environmental and Evolutionary Sciences; Universidad Austral de Chile; Valdivia; Chile
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