What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Elliott, Tyler A.; Gregory, T. Ryan

doi:10.1098/rstb.2014.0331

Cited by 237 publications

(251 citation statements)

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“…This difference may simply be due to experimental error and slight differences in the fluorescence Salemaa and Kamaltynov (1994) found little variation in chromosome number (n=26 or n=32 chromosomes for 13% and 39% of the described Baikal species and genera respectively, including 12 of the genera in the present study), suggesting that differences in genome size may be the result of some other process. This is likely to be the proliferation of repetitive DNA such as transposable elements, which are more abundant in larger genomes (Elliott et al 2015a(Elliott et al , 2015b. Investigation of the other 87% of described species for which chromosome data does not exist will provide further evidence to either support or reject polyploidy as a mechanism which explains the differences in genome size observed here.…”

Section: Discussionmentioning

confidence: 75%

Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia

Jeffery

Yampolsky

Gregory

2017

Genome

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Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans. Specifically, we report genome size estimates for 36 species of Baikal amphipods, and examine the relationship between genome size, body size, and the maximum depths at which the amphipods are found in the lake. Genome sizes ranged nearly 8-fold in this sample of amphipod species, from 2.15 to 16.63 pg, and there were significant, positive, phylogenetically corrected relationships between genome size, body size, maximum depth, and diversification rate among these species. Our results suggest that major genomic changes, including transposable element proliferation, have accompanied speciation that was driven by selection for differences in body size and habitat preference in Lake Baikal amphipods.

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Section: Discussionmentioning

confidence: 75%

Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia

Jeffery

Yampolsky

Gregory

2017

Genome

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“…These differences may arise from the fundamental changes in the population genetic environment that accompanied the origin of eukaryotes, ranging from increased cell size (and concomitant reduction in population densities) to the evolution of meiosis and sex. The relative contributions of genetic drift [54], mutation [55] and selection [56,57]-perhaps at multiple levels [58]-to the origin and evolution of eukaryotes and their genomes remains a fascinating area of debate, and broad comparative data of the type presented by Elliott & Gregory [53] will continue to play an important role in contrasting the predictions of the leading hypotheses.…”

Section: Eukaryotic Genome Evolution From Withinmentioning

confidence: 99%

Changing ideas about eukaryotic origins

Williams

Embley

2015

Phil. Trans. R. Soc. B

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“…genome size evolution | DNA loss | transposable elements | amniotes | flight T he nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate (1)(2)(3)(4)(5)(6)(7). Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) (3).…”

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Dynamics of genome size evolution in birds and mammals

Kapusta

Suh

Feschotte

2017

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

369

358

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Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.genome size evolution | DNA loss | transposable elements | amniotes | flight T he nature and relative importance of the molecular mechanisms and evolutionary forces underlying genome size variation has been the subject of intense research and debate (1-7). Variation in genome sizes may not always occur at a level where natural selection is strong enough to prevent genetic drift to determine their fate (neutral or effectively neutral variation) (3). Additionally, the fixation probability of slightly deleterious deletions or insertions would be higher in species with smaller effective population sizes, where natural selection acts less efficiently (3,8). On the other hand, a number of correlative associations between genome size and phenotypic traits, such as cell size (9, 10) and metabolic rate associated with powered flight (11, 12), suggest that natural selection and adaptive processes also shape genome size evolution. Teasing apart the relative importance of these two forces (drift and selection) requires a better understanding of the mode and processes by which DNA is gained and lost over long evolutionary periods in different taxa. Thus, establishing an integrated view of the contribution of gain and loss of DNA to genome size variation (or lack thereof) remains an important goal in genome biology (e.g., refs. 1, 2, 13, and 14).Most studies of genome size evolution have focused on taxa with extensive variation in genome sizes, such as flowering plants (15)(16)(17)(18)(19)(20), conifers (21), insects (22-...

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What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Cited by 237 publications

References 64 publications

Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia

Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia

Changing ideas about eukaryotic origins

Dynamics of genome size evolution in birds and mammals

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