Genomic parallelism in adaptation to orthogonal environments in sea horses
Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages
Recommendation: posted 01 September 2018, validated 07 September 2018
Studies in speciation genomics have revealed that gene flow is quite common, and that despite this, species can maintain their distinct environmental adaptations. Although researchers are still elucidating the genomic mechanisms by which species maintain their adaptations in the face of gene flow, this often appears to involve few diverged genomic regions in otherwise largely undifferentiated genomes. In this preprint , Riquet and colleagues investigate the genetic structuring and patterns of parallel evolution in the long-snouted seahorse.
Before investigating specific SNPs plausibly associated with adaptation, the authors first describe genome-wide population structure in the long-snouted seahorse. This species is split into five phenotypically similar, but genetically distinct populations. Two populations reside in the Atlantic Ocean and are geographically structured with one north of the Iberian peninsula and the other around the Iberian peninsula. Two other populations are found in the Mediterranean Sea and are structured by the environment as they correspond to marine and lagoon environments. The genetic clustering of lagoon populations in the Mediterranean, despite the substantial geographic distance between them is quite impressive, and worthy of further study. Finally, a fifth population resides in a lagoon-like habitat in the Black Sea.
The authors then investigate patterns of extreme genomic differentiation among populations, and uncover a remarkable pattern of parallel differentiation in these populations. In an outlier scan, Riquet and colleagues find numerous SNPs in one genomic region that separates northern and southern Atlantic populations. Quiet surprisingly, this same genomic region appears to differentiate populations living in marine and lagoon habitats in the Mediterranean. The idea that parallel patterns of genomic differentiation may underlie adaptation to differing environmental scenarios has not yet received much attention. This paper should change that. This paper is particularity impressive in that the authors uncovered this intriguing pattern with under three hundred SNPs. Future genome scale studies will uncover the genomic basis behind this unusual case of parallelism.
 Riquet, F., Liautard-Haag, C., Woodall, L., Bouza, C., Louisy, P., Hamer, B., Otero-Ferrer, F., Aublanc, P., Béduneau, V., Briard, O., El Ayari, T., Hochscheid, S. Belkhir, K., Arnaud-Haond, S., Gagnaire, P.-A., Bierne, N. (2018). Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages. bioRxiv, 161786, ver. 4 recommended and peer-reviewed by PCI Evol Biol. doi: 10.1101/161786
Yaniv Brandvain (2018) Genomic parallelism in adaptation to orthogonal environments in sea horses. Peer Community in Evolutionary Biology, 100056. 10.24072/pci.evolbiol.100056
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.
Evaluation round #1
DOI or URL of the preprint: 10.1101/161786
Version of the preprint: 1
Author's Reply, 13 Jul 2018
Decision by Yaniv Brandvain, posted 13 Jul 2018
Thank you for submitting your preprint to PCI for evaluation. This is a fun process and I hope it improves your manuscript!
I have received feedback from four reviewers who have all found this manuscript to be interesting, but who have all agreed that substantial revision would dramatically improve this manuscript, and would make it publication quality. The reviews should come along with this note. Here is my high level summary and synthesis of their comments plus some of my own.
A major theme is that reviewers (particularly reviewers on and two) were impressed by the care in your analysis of such few markers, however they worried about potential alternative explanations of the data (see comments by reviewers one and three), and hoped for more markers. I agree with the reviewers that there are numerous explanations for the observed results (including strong drift in populations with low diversity, which may make outlier tests less reliable). For example are the treemix results evidence of selection on a few loci or introgression? I think that the current data are ambivalent. I think this paper could be better framed as preliminary results which highlight that this system deserves more attention.
Additionally, reviewer three hoped for a more question driven approach to this system.I am of two minds on this comment. First I agree with the reviewer that hypothesis driven science is quite powerful and makes for compelling writing, however it also feels to me that this manuscript is largely descriptive / exploratory. So I suggest splitting the difference and set up reasonable hypotheses when possible, but don't bend over backwards to make this paper into something it is not. I do agree with the reviewer that this can come across as the 'kitchen sink' so either justify why the difference in the information contained in eg STRUCTURE, PCA, or trees is important to the major argument in the manuscript or be choosy about which belongs in the main text and move redundant analyses to the supp.
Finally, both myself and reviewer four found the paper difficult to follow at times. I suggest rewriting for clarity whenever possible, and (for example) making it clear who the Mediterranean lagoon populations are (I think triangles in Figure 1 meant lagoon, however I could not find this explicitly stated). A less severe version of this is shortening the joint site frequency spectrum to JSFS on line 182 but only defining it as such on line 302. Additionally the manuscript is littered with typos. A healthy dose of editing for typos, clarity of biological questions, and presentation of ideas would drastically improve this paper.
I hope to see a revised version of this manuscript shortly, and I hope that this process improves your paper and the publication process.
I also add an additional review I received that was not conducted via the PCI reviewer system (reviewer 4)
Important contribution of the papers: Broadly, interested in how divergent lineages end up as species. People either think it is natural selection or incompatibilities and that can correlate with clines or mosaics in hybrid zones. Really cool and interesting questions the authors aim to address, but have some concerns.
Reviewer comments Major comments: Story should be linear, and the figures should follow, however throughout the manuscript it is difficult to follow the main story as it jumps around substantially.
Questions: Whole argument about the clines was extremely contrived and confusing to follow.
Difficult to follow the questions addressed in the manuscript
Need more biological background of why focus on the seahorses, for example. Broadly need more background.
Broadly it is difficult to follow the introduction, and the main questions the authors are interested in addressing in the manuscript. Currently it seems that the authors are interested in identifying the genetic variation association with locally adapting to the diverse environments (Lagoons and the sea for examples). I believe that starting with the broad and natural selection/genomic incompatibilities and the “mosaics” and “clines” makes this paper difficult to follow.
Minor comments: Line 124: Misspelled paratrically
Line 124: Would use a different word other than “Patchily” throughout the manuscript as it is difficult to follow.
Line 140: Need to explain in more detail where they get the samples from in the aquaria.
Line 155: Need to state what the reference transcriptome is that was aligned to, explain in more detail the paper that was referenced.
Concern with SNPs measurements, weird ascertainment issues. When developing SNPs from some transcriptomes you are likely to get more common SNPs, which would affect the structure. For example, it may be more common to get SNPs in the lagoon population.
After Line 168: Need to add a sentence about genotyping, we are guessing golden-gate assay was performed? If so I would expand on this in the main manuscript.
Line 169-170: Clever! This is a useful measurement comparing this to other analyses, and this is not done in previous studies.
Figure SI1: Label axis standard, it is difficult to follow what is going on the supplemental figure. Also how did you obtained derived allele frequencies? It was not clear.
Line 179: Oriented = Polarized?
Figure 1: need to define the difference between circle and triangles
Figure 1: remove the little lines where you overlay a figure.
Figure 1 legend: need to include what each color corresponds to; also need to address what yellow corresponds to. Also color choice is not easy to interpret in black/white.
Figure 2C: Need to add axis or add correlations between Figure 2B-2C as it is difficult to follow the big points.
Figure 4: Difficult to follow what the authors are trying to portray in figure 4C.
Figure 5: Difficult to follow the main point of the Figure the authors are trying to convey.
Ordering of the Figures difficult to follow the main story. Should follow a general pattern. Something like Map of study populations first and then the PCA then the structure plot. Also what is the main point of Figure 2C? I would not even include this in the final paper.
Figure 1: Was population 6 dropped from the trees? Also difficult to follow where 20/24 samples were obtained?