Untangling Complex Histories of Genome Mergings in High Polyploids

Brysting, Anne K.; Oxelman, Bengt; Huber, Katharina T.; Moulton, Vincent; Brochmann, Christian

doi:10.1080/10635150701424553

Cited by 83 publications

(86 citation statements)

References 42 publications

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“…Lastly, the homeologous pair was always fixed to cluster together in all orthogroups by not allowing any speciation after duplication scenarios. The latter would entail identifying the correct orthology relationships in sets of outparalogs, which is notoriously difficult (Koonin 2005;Brysting et al 2007). …”

Section: Orthogroup Constructionmentioning

confidence: 99%

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

et al. 2014

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Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous-Paleogene (K-Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K-Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.

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Section: Orthogroup Constructionmentioning

confidence: 99%

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

et al. 2014

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“…Because of the trouble of using molecular data in phylogenetic analyses of polyploid species (RousseauGueutin et al, 2009), a method recommended to reduce the negative effect of polyploidy on reconstructing evolutionary history is to use the low-copy nuclear genes. Furthermore, phylogenetic analyses of mitochondrial and/or low-copy nuclear genes have shed light on the evolution of polyploids (Brysting et al, 2007;Evans et al, 2004Evans et al, , 2005Fortune et al, 2007;Machordom and Doadrio, 2001;Marhold and Lihová, 2006;Sang, 2002;Tsigenopoulos et al, 2002). The nuclear recombination activating gene 2 (RAG2) encodes components of the recombinase involved in recombination of immunoglobin and T-cell receptor genes and appears as conserved single copy in zebrafish (Willett et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Wang

Gan

et al. 2016

Sci. China Life Sci.

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Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.Cyprininae, polyploid, schizothoracins, the Tibetan Plateau, diversifications Citation:Wang, X., Gan, X., Li J., Chen, Y., and He, S. (2016). Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau.

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“…However, the often relatively low variation in cpDNA at the intraspecific level, and the susceptibility of the commonly used nuclear ribosomal internal transcribed spacer (nrITS) region to concerted evolution (12,13), have limited the precision with which allopolyploidy can be identified. In contrast, the use of low-copy nuclear genes can provide more information when particular gene copies in allopolyploids can be linked with genes in the maternal and paternal lineages (14)(15)(16)(17)(18). Despite technical difficulties in identifying appropriate markers and in comparing proper orthologs, several useful nuclear genes have been tested in studies of allopolyploidy (16).…”

mentioning

confidence: 99%

Allopolyploid speciation inPersicaria(Polygonaceae): Insights from a low-copy nuclear region

Kim

Sultan

Donoghue

2008

Proc. Natl. Acad. Sci. U.S.A.

100

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Using a low-copy nuclear gene region (LEAFY second intron) we show multiple instances of allopolyploid speciation in Persicaria (Polygonaceae), which includes many important weeds. Fifteen species seem to be allopolyploids, which is higher than the number found in previous comparisons of chloroplast DNA and nuclear ribosomal internal transcribed spacer (nrITS) phylogenies. This underestimation of the extent of allopolyploidy is due in at least three cases to homogenization of nrITS toward the maternal lineage. One of the diploid species, P. lapathifolia, has been involved in at least six cases of allopolyploid speciation. Of the diploids, this species is the most widespread geographically and ecologically and also bears more numerous and conspicuous flowers, illustrating ecologic factors that may influence hybridization frequency. With a few exceptions, especially the narrowly endemic hexaploid, P. puritanorum, the allopolyploid species also are widespread, plastic, ecological generalists. Hybridization events fostered by human introductions may be fueling the production of new species that have the potential to become aggressive weeds.hybridization ͉ LEAFY intron ͉ phylogeny ͉ Polygonum ͉ invasive species

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Untangling Complex Histories of Genome Mergings in High Polyploids

Cited by 83 publications

References 42 publications

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Allopolyploid speciation inPersicaria(Polygonaceae): Insights from a low-copy nuclear region

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