Agreeing to disagree, some ironies, disappointing scientific practice and a call for better: reply to The poor performance of TMM on microRNA-Seq

Agreeing to disagree, some ironies, disappointing scientific practice and a call for better: reply to The poor performance of TMM on microRNA-Seq
Mark D. Robinson
(Submitted on 27 May 2013)

This letter is a response to a Divergent Views article entitled “The poor performance of TMM on microRNA-Seq” (Garmire and Subramaniam 2013), which was a response to our Divergent Views article entitled “miRNA-seq normalization comparisons need improvement” (Zhou et al. 2013). Using reproducible code examples, we showed that they incorrectly used our normalization method and highlighted additional concerns with their study. Here, I wish to debunk several untrue or misleading statements made by the authors (hereafter referred to as GS) in their response. Unlike GSs, my claims are supported by R code, citations and email correspondences. I finish by making a call for better practice.

Response to No gene-specific optimization of mutation rate in Escherichia coli

Response to No gene-specific optimization of mutation rate in Escherichia coli
Inigo Martincorena, Nicholas M. Luscombe
(Submitted on 7 May 2013)

In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this claim they first attempt to calculate the selective advantage of a local reduction in the mutation rate and conclude that it is not strong enough to be favoured by selection. Second, they analyse the distribution of 166 mutations from a wild-type E. coli K12 MG1655 strain and 1,346 mutations from a repair-deficient strain, and claim to find a positive association between transcription and mutation rate rather than the negative association that we reported. Here we respond to this communication. Briefly, we explain how the long-standing theory of mutation-modifier alleles supports the evolution of local mutation rates within a genome by mechanisms acting on sufficiently large regions of a genome, which is consistent with our original observations [3,4]. We then explain why caution must be exercised when comparing mutations from repair deficient strains to data from wild-type strains, as different mutational processes dominate these conditions. Finally, a reanalysis of the data used by Zhang and Chen with an alternative expression dataset reveals that their conclussions are unreliable.

Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al

Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al
Melissa A. Wilson Sayres
(Submitted on 22 Apr 2013)

Mendez et al. recently report the identification of a Y chromosome lineage from an African American that is an outgroup to all other known Y haplotypes, and report a time to most recent common ancestor, TMRCA, for human Y lineages that is substantially longer than any previous estimate. The identification of a novel Y haplotype is always exciting, and this haplotype, in particular, is unique in its basal position on the Y haplotype tree. However, at 338 (237-581) thousand years ago, kya, the extremely ancient TMRCA reported by Mendez et al. is inconsistent with the known human fossil record (which estimate the age of anatomically modern humans at 195 +- 5 kya), with estimates from mtDNA (176.6 +- 11.3 kya, and 204.9 (116.8-295.7) kya) and with population genetic theory. The inflated TMRCA can quite easily be attributed to the extremely low Y chromosome mutation rate used by the authors.

Our paper: Epistasis not needed to explain low dN/dS

This guest post is by Joshua Plotkin on his group’s paper McCandlish et al. Epistasis not needed to explain low dN/dS arXived here.

Our lab has recently begun to post research pre-prints on arXiv. All members of the group enthusiastically support this trend, both within our own group and within the broader scientific community. The merits of sharing pre-prints have been described elsewhere. The benefits of pre-prints are so immediately apparent, I feel, that there is no need to add further verses to the praises that have already been sung.

Recently, however, my research group and I faced an unusual and difficult question: whether we should post a pre-print that does not describe primary research, but rather is a critique of a recent paper published by another group – a paper on the role of epistasis in molecular evolution from the group led by Fyodor Kondrashov. My group and I have never before written such a commentary; and so I faced this choice with some uncertainty. Here are some thoughts on our group’s decision to write the commentary and to post it to arXiv.

Kondrashov’s group is at the vanguard of contemporary research in molecular evolution. In this particular paper from his group, Breen et al. contend that epistasis is “pervasive throughout protein evolution”; a view that I mostly support and indeed have expressed, in a more limited scope, in several publications and commentaries (e.g. here, here, and here). However, in discussing the paper by Breen et al. over lunch, our research group came to the consensus that their argument is logically flawed. Breen et al. reached their conclusion because the dN/dS values observed in some genes are much lower than their expectation in the absence of epistasis. But when calculating the expected dN/dS ratio in the absence of epistasis, Breen et al. assumed that all amino acids observed in a protein alignment at any particular position have equal fitness. This assumption is unrealistic because, simply, some amino acids may be more fit than others. When we relaxed this unrealistic assumption, we found that the observed dN/dS values and the observed patterns of amino acid diversity at each site are perfectly consistent with a non-epistatic model of protein evolution, for all the nuclear and chloroplast genes in the Breen et al. dataset (but, interestingly, not for their mitochondrial genes).

In an ideal world, scientific disagreements would be resolved by straightforward transactions based solely on logic and data. But in reality, such disagreements inevitably involve intellectual biases, not to mention personalities, politics, reputations, et cetera. In fact, we (my research group and I) are colleagues and admirers of Kondrashov and his comrades (these two papers of his are among our favorites). Why risk our collegiality by publishing a critique on arXiv?

The answer is two-fold. First, we are passionate about understanding molecular evolution, both as individuals and within the context of a scientific community – and we believe this exchange will advance that understanding. Second, we have had extensive email correspondences with Fedya about the scientific issues at hand. These correspondences have been completely open and straightforward: we have shared our computer code so that Fedya can reproduce our analyses; and Fedya has agreed with our critique, in principle, although he has some reservations and may appreciate subtleties of his data that we do not. In any case, I feel that the scientific exchange has been honest, and it will hopefully avoid the snark that sometimes accompanies such disagreements, and focus instead on the scientific issues at stake.

I wish to thank Graham Coop for inviting me to contribute to Haldane’s Sieve. And thanks of course to my co-authors, including our own fearless leader, David McCandlish.

—Joshua B. Plotkin

N.B.: This blog post is meant as an exchange among scientific colleagues, and not as an advertisement to the media.

Epistasis not needed to explain low dN/dS

Epistasis not needed to explain low dN/dS
In Response to “Epistasis as the primary factor in molecular evolution” by Breen et al. Nature 490, 535-538 (2012)
David M. McCandlish, Etienne Rajon, Premal Shah, Yang Ding, Joshua B. Plotkin
(Submitted on 20 Dec 2012)

An important question in molecular evolution is whether an amino acid that occurs at a given position makes an independent contribution to fitness, or whether its effect depends on the state of other loci in the organism’s genome, a phenomenon known as epistasis. In a recent letter to Nature, Breen et al. (2012) argued that epistasis must be “pervasive throughout protein evolution” because the observed ratio between the per-site rates of non-synonymous and synonymous substitutions (dN/dS) is much lower than would be expected in the absence of epistasis. However, when calculating the expected dN/dS ratio in the absence of epistasis, Breen et al. assumed that all amino acids observed in a protein alignment at any particular position have equal fitness. Here, we relax this unrealistic assumption and show that any dN/dS value can in principle be achieved at a site, without epistasis. Furthermore, for all nuclear and chloroplast genes in the Breen et al. dataset, we show that the observed dN/dS values and the observed patterns of amino acid diversity at each site are jointly consistent with a non-epistatic model of protein evolution.