Elusive data underlying debate at the prokaryote-eukaryote divide

Abstract

BackgroundThe origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature.ResultsWe have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure.ConclusionThe data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution.ReviewersThis article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.

Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells

“…Our reanalysis lead to a slightly improved statistical fit of the ribosome number – cell volume scaling relationship, although not significantly so. Contrary to the claims of Gerlitz et al [1], there were no systematic errors. Contrary to the claims of Gerlitz et al [1] the original version of our paper is available at eLife, at https://elifesciences.org/articles/20437v1.…”

“…Their contention is that many of the cell-volume data in Lynch and Marinov [8] do not exist. Confusion was caused by our failure to note that the citations for these data were contained in tables other than the specific one that Gerlitz et al [1] focused on, which pertained to ribosome content. These issues are clarified in Lynch and Marinov [9].…”

“…Three months prior to Gerlitz et al [1], we published a reevaluation and more thorough annotation of the data sources to which they refer [9]. Prior to embarking on their mission, these authors could have sought clarification by communicating directly with us, but did not do so.…”

“…Rather than providing scientific arguments relevant to the debate about mitochondria and the limitations of eukaryotic bioenergetics, Gerlitz et al [1] question the existence of the data upon which our analyses were based. Their contention is that many of the cell-volume data in Lynch and Marinov [8] do not exist.…”

Revisiting the hypothesis of an energetic barrier to genome complexity between eukaryotes and prokaryotes

“…However, as with Lynch & Marinov, our study supports the conclusion that power per gene hardly contributes to the prokaryote-eukaryote divide. In addition, the study of Lynch & Marinov [11] was criticized in terms of elusive data and reproducibility [38]; however, this was caused by the authors' failure to note the citations for these data [39]. This indicates that access to open data is also important for debate in the prokaryote-eukaryote divide.…”