Mutations are the primary source of genetic variation, and there is an obvious interest in characterizing and understanding the processes by which they appear. One particularly important question is the relative abundance, and nature, of replication-dependent and replication-independent mutations - the former arise as cells replicate due to DNA polymerization errors, whereas the latter are unrelated to the cell cycle. A recent experimental study in fission yeast identified a signature of mutations in quiescent (=non-replicating) cells: the spectrum of such mutations is characterized by an enrichment in insertions and deletions (indels) compared to point mutations, and an enrichment of deletions compared to insertions [2].
What Achaz et al. [1] report here is that the very same signature is detectable in humans. This time the approach is indirect and relies on two key aspects of mammalian reproduction biology: (1) oocytes remain quiescent over most of a female's lifespan, whereas spermatocytes keep dividing after male puberty, and (2) X chromosome, Y chromosome and autosomes spend different amounts of time in a female vs. male context. In agreement with the yeast study, Achaz et al. show that in humans the male-associated Y chromosome, for which quiescence is minimal, has by far the lowest ratios of indels to point mutations and of deletions to insertions, whereas the female-associated X chromosome has the highest. This is true both of variants that are polymorphic among humans and of fixed differences between humans and chimpanzees.
So we appear to be here learning about an important and general aspect of the mutation process. The authors suggest that, to a large extent, chromosomes tend to break in pieces at a rate that is proportional to absolute time - because indels in quiescent stage presumably result from double-strand DNA breaks. A very recent analysis of numerous mother-father-child trios in humans confirms this prediction in demonstrating an effect of maternal age, but not of paternal age, on the recombination rate [3]. This result also has important implications with respect to the interpretation of substitution rate variation among taxa and genomic compartments, particularly mitochondrial vs. nuclear, and their relationship with the generation time and longevity of organisms (e.g. [4]).

References

[1] Achaz, G., Gangloff, S., and Arcangioli, B. (2019). The quiescent X, the replicative Y and the Autosomes. BioRxiv, 351288, ver. 3 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/351288
[2] Gangloff, S., Achaz, G., Francesconi, S., Villain, A., Miled, S., Denis, C., and Arcangioli, B. (2017). Quiescence unveils a novel mutational force in fission yeast. eLife, 6:e27469. doi: 10.7554/eLife.27469
[3] Halldorsson, B. V., Palsson, G., Stefansson, O. A., Jonsson, H., Hardarson, M. T., Eggertsson, H. P., … Stefansson, K. (2019). Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science, 363: eaau1043. doi: 10.1126/science.aau1043
[4] Saclier, N., François, C. M., Konecny-Dupré, L., Lartillot, N., Guéguen, L., Duret, L., … Lefébure, T. (2019). Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods. Molecular Biology and Evolution, in press. doi: 10.1093/molbev/msy247

Koutsovoulos et al. [1] have generated and analysed the first population genomic dataset in root-knot nematode Meloidogyne incognita. Why is this interesting? For two major reasons. First, M. incognita has been documented to be apomictic, i.e., to lack any form of sex. This is a trait of major evolutionary importance, with implications on species adaptive potential. The study of genome evolution in asexuals is fascinating and has the potential to inform on the forces governing the evolution of sex and recombination. Even small amounts of sex, however, are sufficient to restore most of the population genetic properties of true sexuals [2]. Because rare events of sex can remain undetected in the field, to confirm asexuality in M. incognita using genomic data is an important step. The second reason why M. incognita is of interest is that this nematode is one of the most harmful pests currently living on earth. M. incognita feeds on the roots of many cultivated plants, including tomato, bean, and cotton, and has been of major agricultural importance for decades. A number of races were defined based on host specificity. These have played a key role in attempts to control the dynamic of M. incognita populations via crop rotations. Races and management strategies so far lack any genetic basis, hence the second major interest of this study.
The authors newly sequenced the full genome of eleven strains from Brazil and added nine already available samples from Africa and North-America. They report that, in all likelihood, M. incognita is indeed a purely asexual species. This is supported by (i) the confirmation that the genome is in its major part haploid, and (ii) a spectacularly high level of linkage disequilibrium, which does not decline with genetic distance between loci at a 100kb scale. The absence of sex and recombination is associated in M. incognita with a remarkably low amount of genetic diversity - one order of magnitude less than in typical sexual nematodes - and an heavy load of deleterious mutations, as measured by the ratio of non-synonymous (=amino-acid changing) to synonymous (=amino-acid conservative) diversity in coding sequences. The other important result of this study is that the population substructure in M. incognita is in no way related to host races or geography. The tree genetic clusters that are identified include strains from several continents and feeding on a diversity of host plants.
The implications of this work are numerous. First, the results suggest that M. incognita is an ancient asexual. Asexuality, which was here demonstrated via linkage disequilibrium analysis, must be ancient enough for diploidy (or, in this case, maybe triploidy) to have been lost - i.e., formerly homologous chromosomes have accumulated enough mutations to be assembled as distinct entities. So we are not talking about a highly successful clone having recently spread the world - rather a long-term obligate parthenogen. Asexual organisms are deprived of the source of genetic variation offered by recombination, which is why asexuality is thought to be an evolutionary dead-end. Long-term asexuals are uncommon and even the most famous ones, bdelloid rotifers, are suspected to experience between-individual genetic transfers [3]. M. incognita is apparently a true 'evolutionary scandal', and as such deserves particular attention from molecular evolutionary geneticists.
The lack of any host race effect on the genetic diversity of M. incognita is another important finding. So-called 'races' have largely contributed to shape researchers' view of the structure of the species so far. This study demonstrates that a mental effort is now needed to forget about races, and consider host-specificity for what it is - a phenotypic trait. This result implies that many host shifts must have independently occurred in the three M. incognita genetic lineages, suggesting an arms race between plants and nematodes, which in the absence of sex and recombination must be entirely mutation-driven on the nematode side. Genes functionally involved in the arms race might therefore be expected to have experienced convergent evolution, if distinct M. incognita lineages have adopted the same solutions to overcome plant defenses. The present study paves the way for such a genome scan. The authors rightly discuss that the strong adaptive potential of M. incognita, at least in terms of host shift, despite no sex and tiny amounts of genetic diversity, is a paradox that would deserve to be further investigated.

References

[1] Koutsovoulos, G. D., Marques, E., Arguel, M. J., Duret, L., Machado, A. C. Z., Carneiro, R. M. D. G., Kozlowski, D. K., Bailly-Bechet, M., Castagnone-Sereno, P., Albuquerque, E. V., & Danchin, E. G. J. (2019). Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode plant pest. bioRxiv, 362129, ver. 5, peer-reviewed and recommended by Peer Community in Evolutionary Biology. doi: 10.1101/362129
[2] Hartfield, M. (2016). Evolutionary genetic consequences of facultative sex and outcrossing. Journal of evolutionary biology, 29(1), 5-22. doi: 10.1111/jeb.12770
[3] Debortoli, N., Li, X., Eyres, I., Fontaneto, D., Hespeels, B., Tang, C. Q., Flot, J. F. & Van Doninck, K. (2016). Genetic exchange among bdelloid rotifers is more likely due to horizontal gene transfer than to meiotic sex. Current Biology, 26(6), 723-732. doi: 10.1016/j.cub.2016.01.031

Estimating the genetic and environmental components of variation in reproductive success is crucial to understanding the adaptive potential of populations to environmental change. To date, the heritability of lifetime reproductive success (fitness) has been estimated in a handful of wild animal population, mostly in mammals and birds, but has never been estimated for a marine species. The primary reason that such estimates are lacking in marine species is that most marine organisms have a dispersive larval phase, making it extraordinarily difficult to track the fate of offspring from one generation to the next.
In this study, Salles et al. [1] use an unprecedented 10 year data set for a wild population of orange clownfish (Amphiprion percula) to estimate the environmental, maternal and additive genetic components of life time reproductive success for the self-recruiting portion of the local population. Previous studies show that over 50% of juvenile clownfish recruiting to the population of clownfish at Kimbe Island (Kimbe Bay, PNG) are natal to the population. In other words, >50% of the juveniles recruiting to the population at Kimbe Island are offspring of parents from Kimbe Island. The identity and location of every adult clownfish in the Kimbe Island population was tracked over 10 years. At the same time newly recruiting juveniles were collected at regular intervals (biennially) and their parentage assigned with high confidence by 22 polymorphic microsatellite loci. Salles et al. then used a pedigree comprising 1735 individuals from up to 5 generations of clownfish at Kimbe Island to assess the contribution of every breeding pair of clownfish to self-recruitment within the local population. Because clownfish are site attached and live in close association with a host sea anemone, it was also possible to examine the contribution of reef location and host anemones species (either Heteractis magnifica or Stichodactyla gigantea) to reproductive success within the local population.
The study found that breeders from the eastern side of Kimbe Island, and mostly inhabiting S. gigantea sea anemones, produced more juveniles that recruited to the local population than breeders from other location around the island, or inhabiting H. magnifica. In fact, host anemone species and geographic location explained about 97% of the variance in reproductive success within the local population (i.e. excluding successful recruitment to other populations). By contrast, maternal and additive genetic effects explained only 1.9% and 1.3% of the variance, respectively. In other words, reef location and the species of host anemone inhabited had an overwhelming influence on the long-term contribution of breeding pairs of clownfish to replenishment of the local population. This overwhelming effect of the local habitat on reproductive success means that the population is potentially susceptible to rapid environmental changes - for example if S. giganta sea anemones are disproportionately susceptible to global warming, or reef habitats on the eastern side of the island are more susceptible to disturbance. By contrast, the small component of additive genetic variance in local reproductive success translated into low heritability and evolvability of lifetime reproductive success within the local population, as predicted by theory [2] and observed in some terrestrial species. Consequently, fitness would evolve slowly to environmental change.
Establishing the components of variation in fitness in a wild population of marine fishes is an astonishing achievement, made possible by the unprecedented long-term individual-level monitoring of the entire population of clownfish at Kimbe Island. A next step in this research would be to include other clownfish populations that are demographically and genetically connected to the Kimbe Island population through larval dispersal. It would be intriguing to establish the environmental, maternal and additive genetic components of reproductive success in the dispersing part of the Kimbe Island population, to see if this potentially differs among breeders who contribute more or less to replenishment within the local population.

References

[1] Salles, O. C., Almany, G. R., Berumen, M.L., Jones, G. P., Saenz-Agudelo, P., Srinivasan, M., Thorrold, S. R., Pujol, B., Planes, S. (2019). Strong habitat and weak genetic effects shape the lifetime reproductive success in a wild clownfish population. Zenodo, 3476529, ver. 3 peer-reviewed and recommended by Peer Community In Evolutionary Biology. doi: 10.5281/zenodo.3476529
[2] Fisher, R.A. (1930). The genetical theory of natural selection. Clarendon Press, Oxford, U.K.

Artificial selection experiments are key experiments in evolutionary biology. The demonstration that application of selective pressure across multiple generations results in heritable phenotypic changes is a tangible and reproducible proof of the evolution by natural selection.
Artificial selection experiments are used to evaluate the joint effects of selection on multiple traits, their genetic covariances and differences in responses in different environments. Most studies on artificial selection experiments report and base their analyses on phenotypic changes [1]. More recently, changes in allele frequency and other patterns of molecular genetic diversity have been used to identify genomic locations where selection has had an effect. However, so far the changes in gene expression have not been in the focus of artificial selection experiment studies (see [2] for an example though).
In plants, one of the most famous artificial selection experiments is the Illinois Corn Experiment where maize (Zea mays) is selected for oil and protein content [3], but in addition, similar experiments have been conducted also for other traits in maize. In Saclay divergent selection experiment [4] two maize inbred lines (F252 and MBS847) have been selected for early and late flowering for 13 generations, resulting in two week difference in flowering time.
In ”Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network ” [5] Maud Tenaillon and her coworkers study the gene expression differences among these two independently selected maize populations. Their experiments cover two years in field conditions and they use samples of shoot apical meristem at three different developmental stages: vegetative, transitioning and reproductive. They use RNA-seq transcriptome level differences and qRT-PCR for gene expression pattern investigation. The work is continuation to earlier genetic and phenotypic studies on the same material [4, 6].
The reviewers and I agree that dataset is unique and its major benefit is that it has been obtained from field conditions similar to those that species may face under natural setting during selection. Their tissue sampling is supported by flowering time phenotypic observations and covers the developmental transition stage, making a good effort to identify key transcriptional and phenotypic changes and their timing affected by selection.
Tenaillon et al. [5] identify more than 2000 genes that are differentially expressed among early and late flowering populations. Expectedly, they are enriched for known flowering time genes. As they point out, differential expression of thousands of genes does not mean that they all were independently affected by selection, but rather that the whole transcriptional network has shifted, possibly due to just few upstream or hub-genes. Also, the year-to-year variation had smaller effect in gene expression compared to developmental stage or genetic background, possibly indicating selection for stability across environmental fluctuation for such an important phenotype as flowering time.
Another noteworthy observation is that they find convergent patterns of transcriptional changes among the two selected lines. 115 genes expression patterns are shifted due to selection in both genetic backgrounds. This convergent pattern can be a result of either selection on standing variation or de novo mutations. The data does not allow testing which process is underlying the observed convergence. However, their results show that this is an interesting future question that can be addressed using genotype and gene expression data from the same ancestral and derived material and possibly their hybrids.

References

[1] Hill, W. G., & Caballero, A. (1992). Artificial selection experiments. Annual Review of Ecology and Systematics, 23(1), 287-310. doi: 10.1146/annurev.es.23.110192.001443
[2] Konczal, M., Babik, W., Radwan, J., Sadowska, E. T., & Koteja, P. (2015). Initial molecular-level response to artificial selection for increased aerobic metabolism occurs primarily through changes in gene expression. Molecular biology and evolution, 32(6), 1461-1473. doi: 10.1093/molbev/msv038
[3] Moose, S. P., Dudley, J. W., & Rocheford, T. R. (2004). Maize selection passes the century mark: a unique resource for 21st century genomics. Trends in plant science, 9(7), 358-364. doi: 10.1016/j.tplants.2004.05.005
[4] Durand, E., Tenaillon, M. I., Ridel, C., Coubriche, D., Jamin, P., Jouanne, S., Ressayre, A., Charcosset, A. and Dillmann, C. (2010). Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds. BMC evolutionary biology, 10(1), 2. doi: 10.1186/1471-2148-10-2
[5] Tenaillon, M. I., Seddiki, K., Mollion, M., Le Guilloux, M., Marchadier, E., Ressayre, A. and Dillmann C. (2019). Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network. BioRxiv, 461947 ver. 5 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/461947
[6] Durand, E., Tenaillon, M. I., Raffoux, X., Thépot, S., Falque, M., Jamin, P., Bourgais A., Ressayre, A. and Dillmann, C. (2015). Dearth of polymorphism associated with a sustained response to selection for flowering time in maize. BMC evolutionary biology, 15(1), 103. doi: 10.1186/s12862-015-0382-5

Phylogenetic trees can be used to extract information about the process of diversification that has generated them. The most common approach to conduct this inference is to rely on a likelihood, defined here as the probability of generating a dated tree T given a diversification model (e.g. a birth-death model), and then use standard maximum likelihood. This idea has been explored extensively in the context of the so-called diversification studies, with many variants for the models and for the questions being asked (diversification rates shifting at certain time points or in the ancestors of particular subclades, trait-dependent diversification rates, etc).
However, all this assumes that the dated tree T is known without error. In practice, trees (that is, both the tree topology and the divergence times) are inferred based on DNA sequences, possibly combined with fossil information for calibrating and informing the divergence times. Molecular dating is a delicate exercise, however, and much more so in fact than reconstructing the tree topology. In particular, a mis-specificied model for the relaxed molecular clock, or a mis-specifiied prior, can have a substantial impact on the estimation of divergence dates - which in turn could severely mislead the inference about the underlying diversification process. This thus raises the following question: would that be possible to conduct inference and testing of diversification models without having to go through the dangerous step of molecular dating?
In his article ""Probabilities of tree topologies with temporal constraints and diversification shifts"" [1], Gilles Didier introduces a recursive method for computing the probability of a tree topology under some diversification model of interest, without knowledge of the exact dates, but only interval constraints on the dates of some of the nodes of the tree. Such interval constraints, which are derived from fossil knowledge, are typically used for molecular dating: they provide the calibrations for the relaxed clock analysis. Thus, what is essentially proposed by Gilles Didier is to use them in combination with the tree topology only, thus bypassing the need to estimates divergence times first, before fitting a diversification model to a phylogenetic tree.
This article, which is primarily a mathematical and algorithmic contribution, is then complemented with several applications: testing for a diversification shift in a given subclade of the phylogeny, just based on the (undated) tree topology, with interval constraints on some of its internal nodes; but also, computing the age distribution of each node and sampling on the joint distribution on node ages, conditional on the interval constraints. The test for the presence of a diversification shift is particularly interesting: an application to simulated data (and without any interval constraint in that case) suggests that the method based on the undated tree performs about as well as the classical method based on a dated tree, and this, even granting the classical approach a perfect knowledge of the dates - given that, in practice, one in fact relies on potentially biased estimates. Finally, an application to a well-known example (rate shifts in cetacean phylogeny) is presented.
This article thus represents a particularly meaningful contribution to the methodology for diversification studies; but also, for molecular dating itself: it is a well known problem in molecular dating that computing and sampling from the conditional distributions on node ages, given fossil constraints, and more generally understanding and visualizing how interval constraints on some nodes of the tree impact the distribution at other nodes, is a particularly difficult exercise. For that reason, the algorithmic routines presented in the present article will be useful in this context as well.

References

[1] Didier, G. (2020) Probabilities of tree topologies with temporal constraints and diversification shifts. bioRxiv, 376756, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/376756