Strange reproductive modes and population genetics
Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula
Recommendation: posted 01 February 2022, validated 22 March 2022
There are many organisms that are asexual or have unusual modes of reproduction. One such quasi-sexual reproductive mode is androgenesis, in which the offspring, after fertilization, inherits only the entire paternal nuclear genome. The maternal genome is ditched along the way. One group of organisms which shows this mode of reproduction are clams in the genus Corbicula, some of which are androecious, while others are dioecious and sexual. The study by Vastrade et al. (2022) describes population genetic patterns in these clams, using both nuclear and mitochondrial sequence markers.
In contrast to what might be expected for an asexual lineage, there is evidence for significant genetic mixing between populations. In addition, there is high heterozygosity and evidence for polyploidy in some lineages. Overall, the picture is complicated! However, what is clear is that there is far more genetic mixing than expected. One possible mechanism by which this could occur is 'nuclear capture' where there is a mixing of maternal and paternal lineages after fertilization. This can sometimes occur as a result of hybridization between 'species', leading to further mixing of divergent lineages. Thus the group is clearly far from an ancient asexual lineage - recombination and mixing occur with some regularity.
The study also analyzed recent invasive populations in Europe and America. These had reduced genetic diversity, but also showed complex patterns of allele sharing suggesting a complex origin of the invasive lineages.
In the future, it will be exciting to apply whole genome sequencing approaches to systems such as this. There are challenges in interpreting a handful of sequenced markers especially in a system with polyploidy and considerable complexity, and whole-genome sequencing could clarify some of the outstanding questions,
Overall, this paper highlights the complex genetic patterns that can result through unusual reproductive modes, which provides a challenge for the field of population genetics and for the recognition of species boundaries.
Vastrade M, Etoundi E, Bournonville T, Colinet M, Debortoli N, Hedtke SM, Nicolas E, Pigneur L-M, Virgo J, Flot J-F, Marescaux J, Doninck KV (2022) Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula. bioRxiv, 590836, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/590836
Chris Jiggins (2022) Strange reproductive modes and population genetics. Peer Community in Evolutionary Biology, 100137. https://doi.org/10.24072/pci.evolbiol.100137
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. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/590836
Version of the preprint: 2
Author's Reply, 18 Jan 2022
Decision by Chris Jiggins, posted 19 Nov 2021
This preprint is suitable for a recommendation but the second reviewer makes a number of suggestions which I would like to give the authors a chance to respond to. In particular further attempt to make the discussion more general and more concise would be an improvement.
Reviewed by Simon Henry Martin, 09 Nov 2021
Reviewed by Arnaud Estoup, 04 Nov 2021
Reviewed by anonymous reviewer, 07 Nov 2021
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/590836
Version of the preprint: 1
Author's Reply, 01 Oct 2021
Decision by Chris Jiggins, posted 08 May 2019
The reviews generally accept the broad interest of the paper and the advances, and I agree with this. However, there are some important comments on the paper that need to be addressed. The key comments include: 1) the framing of the paper and making it more appealing to a general audience - it is currently written very much about the Corbicula clams, but it is unclear how it relates to evolutionary processes on other organisms. This needs work both in the introduction and perhaps also in the conclusions - how does the unique reproductive mode affect the genetic variation in these organisms compared to other systems? 2) Clear statement of the hypotheses being tested. This is particularly important - the final paragraph of the introduction focusses on methods used (i.e. Haplowebs) but does not really outline what the paper is trying to test. Could there be a list of specific hypotheses laid out in this paragraph? 3) Clarify nomenclature such as 'egg parasitism' - I agree with the reviewer that this seems a misleading term and request that a better term is devised. 4) Better clarify what is novel in this paper relative to previous work on the same system. There are a number of references to previous studies but it should be clarified which data comes from previous papers (and if published data are not included why was this the case) and which questions can be addressed here that were not addressed before. More specifically, what exactly is novel here apart from the use of a web based method of analysis. I am also concerned about some of the methodological questions raised by reviewers. How many clones were sequenced per individual and why were triploid allele patterns not detected - is this just because too few clones were sequenced. Also clarify the 'remove singletons' option in the Haploweb program. Why were singletons removed? There are a large number of additional minor suggestions that should be addressed in the reviews. Subject to addressing these points I think the manuscript is appropriate for a recommendation. **Additional requirements of the managing board**: As indicated in the 'How does it work?’ section and in the code of conduct, please make sure that: -Data are available to readers, either in the text or through an open data repository such as Zenodo (free), Dryad (to pay) or some other institutional repository. Data must be reusable, thus metadata or accompanying text must carefully describe the data. -Details on quantitative analyses (e.g., data treatment and statistical scripts in R, bioinformatic pipeline scripts, etc.) and details concerning simulations (scripts, codes) are available to readers in the text, as appendices, or through an open data repository, such as Zenodo, Dryad or some other institutional repository. The scripts or codes must be carefully described so that they can be reused. -Details on experimental procedures are available to readers in the text or as appendices. -Authors have no financial conflict of interest relating to the article. The article must contain a "Conflict of interest disclosure" paragraph before the reference section containing this sentence: "The authors of this preprint declare that they have no financial conflict of interest with the content of this article." If appropriate, this disclosure may be completed by a sentence indicating that some of the authors are PCI recommenders: “XXX is one of the PCI XXX recommenders.”