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Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species’ ecology, demography and genetics.

Here, we review the literature on sexual lability in dioecious angiosperm species with well-studied sex chromosomes. We distinguish three types of departures from strict dioecy, concerning either a minority of flowers in some individuals (leakiness) or the entire individual, which can constantly be bisexual or change sex. We found that for only four of the 22 species studied, reports of lability are lacking. The occurrence of lability is only weakly related to sex chromosome characteristics (number of sex-linked genes, age of the non-recombining region). These results contradict the naive idea that lability is an indication of the absence or the recent evolution of sex chromosomes, and thereby contribute to a growing consensus that sex chromosomes do not necessarily fix sex determination once and for all. We discuss some implications of these findings for the evolution of sex chromosomes, and suggest that more species with well-characterized lability should be studied with genomic data and tools.This article is part of the theme issue ‘Sex determination and sex chromosome evolution in land plants’.

We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has lead to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we demonstrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

Research We recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants (12–28 Myr old). Based on the estimated age, we predicted that it should be shared by its sister genus Humulus, which is known also to possess XY chromosomes. Here, we used transcriptome sequencing of an F1 family of H. lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETECTOR. We identified 265 sex-linked genes in H. lupulus, which preferentially mapped to the C. sativa X chromosome. Using phylogenies of sex-linked genes, we showed that a region of the sex chromosomes had already stopped recombining in an ancestor of both species. Furthermore, as in C. sativa, Y-linked gene expression reduction is correlated to the position on the X chromosome, and highly Y degenerated genes showed dosage compensation. We report, for the first time in Angiosperms, a sex chromosome system that is shared by two different genera. Thus, recombination suppression started at least 21–25 Myr ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes (c. 70%), leading to a degenerated Y chromosome info:eu-repo/semantics/publishedVersion

International audience; The genetic basis and evolution of sex determination in dioecious plants is emerging as an active area of research with exciting advances in genome sequencing and analysis technologies. As the sole species within the sister lineage to all other extant flowering plants, Amborella trichopoda is an important model for understanding the evolution and development of flowers. Plants typically produce only male or female flowers, but sex determination mechanisms are unknown for the species. Sequence data derived from plants of natural origin and an F1 mapping population were used to identify sex-linked genes and the nonrecombining region. Amborella trichopoda has a ZW sex determination system. Analysis of genes in a 4 Mb nonrecombining sex-determination region reveals recent divergence of Z and W gametologs, and few Z- and W-specific genes. The sex chromosomes of A. trichopoda evolved less than 16.5 Myr ago, long after the divergence of the extant angiosperms.

Sex determination is poorly understood in plants. Amborella trichopoda is a well-known plant model for evo-devo studies, which is also dioecious (has male and female individuals), with an unknown sex determination mechanism. A. trichopoda is a “sex switcher”, which points to possible environmental factors that act on sex, but populations grown from seed under greenhouse conditions exhibit a 50:50 sex ratio, which indicates the operation of genetic factors. Here, we use a new method (SDpop) to identify sex-linked genes from genotyping data of male and female individuals sampled in the field, and find that A. trichopoda has a ZW sex-chromosome system. The sex-linked genes map to a 4 Mb sex-determining region on chromosome 9. The low extent of ZW divergence suggests these sex chromosomes are of recent origin, which is consistent with dioecy being derived character in the A. trichopoda lineage. Our work has uncovered clearly formed sex chromosomes in a species in which both genetic and environmental factors can influence sex.One Sentence SummaryAmborella trichopoda, a dioecious species in which both genetics and the environment influence sex, possesses a pair of quite recently evolved ZW chromosomes.

Background A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. Results We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. Conclusions We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.

International audience; Reduced visibility of women in science is thought to be one of the causes of their underrepresentation among scientists, in particular at senior positions. Visibility is achieved through publications, and through conference attendance and presentations. Here, we investigated gender differences in visibility at the annual meetings of the Society of Molecular Biology and Evolution. The analysis of meeting programs showed a regular increase in female speakers for the last 16 years. Data on abstract submission suggest that there are no gender-related preferences in the acceptance of contributed presentations at the most recent meetings. However, data collected on-site in 2015 and 2016 show that women asked only ∼25% of the questions, that is, much less than expected given the female attendance. Understanding the reasons for this pattern is necessary for the development of policies that aim to reduce imbalance in visibility.

Dioecy, the coexistence of separate male and female individuals in a population, is a rare but phylogenetically widespread sexual system in flowering plants. While research has concentrated on why and how dioecy evolves from hermaphroditism, the question of why dioecy is rare, despite repeated transitions to it, has received much less attention. Previous phylogenetic and theoretical studies have suggested that dioecy might be an evolutionary dead end. However, recent research indicates that the phylogenetic support for this hypothesis is attributable to a methodological bias and that there is no evidence for reduced diversification in dioecious angiosperms. The relative rarity of dioecy thus remains a puzzle. Here, we review evidence for the hypothesis that dioecy might be rare not because it is an evolutionary dead end, but rather because it easily reverts to hermaphroditism. We review what is known about transitions between hermaphroditism and dioecy, and conclude that there is an important need to consider more widely the possibility of transitions away from dioecy, both from an empirical and a theoretical point of view, and by combining tools from molecular evolution and insights from ecology.

Copepods are the most numerous animals and play an essential role in the marine trophic web and biogeochemical cycles. The genus Oithona is described as having the highest numerical density, as the most cosmopolite copepod and iteroparous. The Oithona male paradox obliges it to alternate feeding (immobile) and mating (mobile) phases. As the molecular basis of this trade-off is unknown, we investigated this sexual dimorphism at the molecular level by integrating genomic, transcriptomic and protein-protein interaction analyses.While a ZW sex-determination system was predicted in O. nana, a fifteen-year time-series in the Toulon Little Bay showed a biased sex ratio toward females (male / female ratio < 0.15±0.11) highlighting a higher mortality in male. Here, the transcriptomic analysis of the five different developmental stages showed enrichment of Lin12-Notch Repeat (LNR) domains-containing proteins coding genes (LDPGs) in male transcripts. The male also showed enrichment in transcripts involved in proteolysis, nervous system development, synapse assembly and functioning and also amino acid conversion to glutamate. Moreover, several male down-regulated genes were involved in the increase of food uptake and digestion. The formation of LDP complexes was detected by yeast two-hybrid, with interactions involving proteases, extracellular matrix proteins and neurogenesis related proteins.Together, these results suggest that the O. nana male hypermotility is sustained by LDP-modulated proteolysis allowing the releases and conversions of amino acid into the excitatory neurotransmitter glutamate. This process could permit new axons and dendrites formation suggesting a sexual nervous system dimorphism. This could support the hypothesis of a sacrificial behaviour in males at the metabolic level.

Cannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide.C. sativais a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. TheC. sativasex chromosomes sequence would improve early sexing and better management of this crop; however, theC. sativagenome projects failed to identify the sex chromosomes so far. Moreover, dioecy in the Cannabaceae family is ancestral,C. sativasex chromosomes are potentially old and thus very interesting to study as little is known about the last steps of sex chromosome evolution in plants. Here we RNA-sequenced aC. sativafamily (2 parents and 10 male and female offspring) and performed a segregation analysis for allC. sativagenes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to aC. sativagenome assembly identified a single chromosome pair with a large non-recombining region. Further analysis of the >500 sex-linked genes revealed thatC. sativahas a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large non-recombining regions and be very differentiated and still be of similar size (homomorphic).

Cannabis sativa–derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY Chromosomes, and only females (XX) are useful for THC production. Identifying the sex chromosome sequence would improve early sexing and better management of this crop; however, the C. sativa genome projects have failed to do so. Moreover, as dioecy in the Cannabaceae family is ancestral, C. sativa sex chromosomes are potentially old and thus very interesting to study, as little is known about old plant sex chromosomes. Here, we RNA-sequenced a C. sativa family (two parents and 10 male and female offspring, 576 million reads) and performed a segregation analysis for all C. sativa genes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified the largest chromosome pair being the sex chromosomes. We found that the X-specific region (not recombining between X and Y) is large compared to other plant systems. Further analysis of the sex-linked genes revealed that C. sativa has a strongly degenerated Y Chromosome and may represent the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large, highly divergent nonrecombining regions, yet still be roughly homomorphic.

International audience

We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical Silene data show that our method identifies 20–35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available., Genome Biology and Evolution, 8 (8), ISSN:1759-6653

Cell aggregates are a tool for in vitro studies of morphogenesis, cancer invasion, and tissue engineering. They respond to mechanical forces as a complex rather than simple liquid. To change an aggregate's shape, cells have to overcome energy barriers. If cell shape fluctuations are active enough, the aggregate spontaneously relaxes stresses (“fluctuation-induced flow”). If not, changing the aggregate's shape requires a sufficiently large applied stress (“stress-induced flow”). To capture this distinction, we develop a mechanical model of aggregates based on their cellular structure. At stress lower than a characteristic stress τ*, the aggregate as a whole flows with an apparent viscosity η*, and at higher stress it is a shear-thinning fluid. An increasing cell–cell tension results in a higher η* (and thus a slower stress relaxation time t c ). Our constitutive equation fits experiments of aggregate shape relaxation after compression or decompression in which irreversibility can be measured; we find t c of the order of 5 h for F9 cell lines. Predictions also match numerical simulations of cell geometry and fluctuations. We discuss the deviations from liquid behavior, the possible overestimation of surface tension in parallel-plate compression measurements, and the role of measurement duration.

1. However, validating these hypotheses has been difficult due to the lack of appropriate tools to measure these parameters. Here we use atomic force microscopy (AFM) to quantify the adhesive and mechanical properties of individual ectoderm, mesoderm and endoderm progenitor cells from gastrulating zebrafish embryos. Combining these data with tissue self-assembly in vitro and the sorting behaviour of progenitors in vivo, we have shown that differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGFβ-signalling (transforming growth factor β), constitutes a key factor that directs progenitor-cell sorting. These results demonstrate a previously unrecognized role for Nodal-controlled cell-cortex tension in germ-layer organization during gastrulation. 2 . Both cell adhesion and contraction have long been implicated in germ-layer formation; however, their relative contribution to these processes is still a matter of debate 3 . We therefore sought to quantify the specific adhesive and mechanical properties of the different progenitor types at the single-cell level and correlate these values to the actual sorting behaviour of progenitors in vitro and in vivo (for generation of different germ-layer progenitor

Hayashi and Carthew (Nature 431 [2004], 647) have shown that the packing of cone cells in the Drosophila retina resembles soap bubble packing, and that changing E- and N-cadherin expression can change this packing, as well as cell shape. The analogy with bubbles suggests that cell packing is driven by surface minimization. We find that this assumption is insufficient to model the experimentally observed shapes and packing of the cells based on their cadherin expression. We then consider a model in which adhesion leads to a surface increase, balanced by cell cortex contraction. Using the experimentally observed distributions of E- and N-cadherin, we simulate the packing and cell shapes in the wildtype eye. Furthermore, by changing only the corresponding parameters, this model can describe the mutants with different numbers of cells, or changes in cadherin expression., revised manuscript; 8 pages, 6 figures; supplementary information not included

Data deposition: During the review process, the SEX-DETector galaxy workflow and associated test datasets are made available on the public galaxy.prabi.fr server. The data as well as the tool interface are visible to anonymous users, but to use them, you should register for an account (“user Register”), and import the data library “SEX-DETector” (“Shared Data Data Libraries”) into your history. More instructions can be found in the “readme” file in this library. The user manual for SEX-DETector is available here: https://lbbe.univ-lyon1.fr/Download-5251.html?lang=en.Paper submitted as a Genome Resource.We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, UV). Sex chromosomes (especially the nonrecombining and repeat-dense Y, W, U and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. However, most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sex-linked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Tests on empirical data show that our method identifies many more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Simulations suggest few individuals are needed for optimal results. For species with unknown sex-determination system, the method can assess the presence and type (XY versus ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimised for sex chomosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organism, including non-model ones for which nothing is known a priori, that can be bred in the lab, is suitable for our method. SEX-DETector is made freely available to the community through a Galaxy workflow.

Bubble monolayers are model systems for experiments and simulations of two-dimensional packing problems of deformable objects. We explore the relation between the distributions of the number of bubble sides (topology) and the bubble areas (geometry) in the low liquid fraction limit. We use a statistical model [M. Durand, Europhys. Lett. 90, 60002 (2010)] which takes into account Plateau laws. We predict the correlation between geometrical disorder (bubble size dispersity) and topological disorder (width of bubble side number distribution) over an extended range of bubble size dispersities. Extensive data sets arising from shuffled foam experiments, surface evolver simulations, and cellular Potts model simulations all collapse surprisingly well and coincide with the model predictions, even at extremely high size dispersity. At moderate size dispersity, we recover our earlier approximate predictions [M. Durand, J. Kafer, C. Quilliet, S. Cox, S. A. Talebi, and F. Graner, Phys. Rev. Lett. 107, 168304 (2011)]. At extremely low dispersity, when approaching the perfectly regular honeycomb pattern, we study how both geometrical and topological disorders vanish. We identify a crystallization mechanism and explore it quantitatively in the case of bidisperse foams. Due to the deformability of the bubbles, foams can crystallize over a larger range of size dispersities than hard disks. The model predicts that the crystallization transition occurs when the ratio of largest to smallest bubble radii is 1.4.

International audience; Comparing species richness in sister clades that differ in a character state is one of the ways to study factors influencing diversification. While most of its applications have focussed on traits that increase diversification, some have been used to study the association of a trait with lower species richness, e.g., the occurrence of dioecy in flowering plants. We show here, using simulations and an analytical model, that the null expectation of equal species richness that is generally used in sister clade comparisons is wrong in the case of a derived trait occurring independently from speciation: one should expect fewer species in the clade with the derived character state when there is no difference in diversification rates. This is due to the waiting time for the derived state to appear, which causes it to occur more often on longer branches. This has the important implication that the probability for a clade to possess the derived state depends on the tree geometry, and thus on species richness: species-poorer clades are more likely to possess the derived state. We develop a statistical test for sister clade comparisons to study the effect of a derived character state. Applying it to a data set of dioecious clades, we find that we cannot confirm earlier work that concluded that dioecy decreases diversification; on the contrary, it seems to be associated to higher species richness than expected. [angiosperms; dioecy; diversification; sister clades; species richness.].

International audience; BACKGROUND AND AIMS: About 6 % of an estimated total of 240 000 species of angiosperms are dioecious. The main precursors of this sexual system are thought to be monoecy and gynodioecy. A previous angiosperm-wide study revealed that many dioecious species have evolved through the monoecy pathway; some case studies and a large body of theoretical research also provide evidence in support of the gynodioecy pathway. If plants have evolved through the gynodioecy pathway, gynodioecious and dioecious species should co-occur in the same genera. However, to date, no large-scale analysis has been conducted to determine the prevalence of the gynodioecy pathway in angiosperms. In this study, this gap in knowledge was addressed by performing an angiosperm-wide survey in order to test for co-occurrence as evidence of the gynodioecy pathway.\n\nMETHODS: Data from different sources were compiled to obtain (to our knowledge) the largest dataset on gynodioecy available, with 275 genera that include at least one gynodioecious species. This dataset was combined with a dioecy dataset from the literature, and a study was made of how often dioecious and gynodioecious species could be found in the same genera using a contingency table framework.\n\nKEY RESULTS: It was found that, overall, angiosperm genera with both gynodioecious and dioecious species occur more frequently than expected, in agreement with the gynodioecy pathway. Importantly, this trend holds when studying different classes separately (or sub-classes, orders and families), suggesting that the gynodioecy pathway is not restricted to a few taxa but may instead be widespread in angiosperms.\n\nCONCLUSIONS: This work complements that previously carried out on the monoecy pathway and suggests that gynodioecy is also a common pathway in angiosperms. The results also identify angiosperm families where some (or all) dioecious species may have evolved from gynodioecious precursors. These families could be the targets of future small-scale studies on transitions to dioecy taking phylogeny explicitly into account.

International audience; In angiosperms, dioecious clades tend to have fewer species than their nondioecious sister clades. This departure from the expected equal species richness in the standard sister clade test has been interpreted as implying that dioecious clades diversify less and has initiated a series of studies suggesting that dioecy might be an 'evolutionary dead end'. However, two of us recently showed that the 'equal species richness' null hypothesis is not valid in the case of derived char acters, such as dioecy, and proposed a new test for sister clade comparisons; preliminary results, using a data set available in the litterature, indicated that dioecious clades migth diversify more than expected. However, it is crucial for this new test to distinguish between ancestral and derived cases of dioecy, a criterion that was not taken into account in the available data set. Here, we present a new data set that was obtained by searching the phylogenetic literature on more than 600 completely dioecious angiosperm genera and identifying 115 sister clade pairs for which dioecy is likely to be derived (including > 50% of the dioecious species). Applying the new sister clade test to this new dataset, we confirm the preliminary result that dioecy is associated with an increased diversification rate, a result that does not support the idea that dioecy is an evolutionary dead end in angiosperms. The traits usually associated with dioecy, that is, an arborescent growth form, abiotic pollination, fleshy fruits or a tropical distribution, do not influence the diversification rate. Rather than a low diversification rate, the observed species richness patterns of dioecious clades seem to be better explained by a low transition rate to dioecy and frequent losses.

Dioecy (i.e. having separate sexes) is a rather rare breeding system in flowering plants. Such rareness may result from a high probability of extinction in dioecious species because of less efficient dispersal and the costs of sexual selection, which are expected to harm dioecious species' survival on the long term. These handicaps should decrease the effective population size (Ne) of dioecious species, which in turn should reduce the efficacy of selection. Moreover, sexual selection in dioecious species is expected to specifically affect some genes, which will evolve under positive selection. The relative contribution of these effects is currently unknown and we tried to disentangle them by comparing sequence evolution between dioecious and non-dioecious species in the Silene genus (Caryophyllaceae), where dioecy has evolved at least twice. For the dioecious species in the section Melandrium, where dioecy is the oldest, we found a global reduction of purifying selection, while on some, male-biased genes, positive selection was found. For section Otites, where dioecy evolved more recently, we found no significant differences between dioecious and non-dioecious species. Our results are consistent with the view that dioecy is an evolutionary dead end in flowering plants, although other scenarios for explaining reduced Ne cannot be ruled out. Our results also show that contrasting forces act on the genomes of dioecious plants, and suggest that some time is required before the genome of such plants bears the footprints of dioecy.

We propose an analytical model for the statistical mechanics of shuffled two-dimensional foams with moderate bubble size polydispersity. It predicts without any adjustable parameters the correlations between the number of sides n of the bubbles (topology) and their areas A (geometry) observed in experiments and numerical simulations of shuffled foams. Detailed statistics show that in shuffled cellular patterns n correlates better with √A (as claimed by Desch and Feltham) than with A (as claimed by Lewis and widely assumed in the literature). At the level of the whole foam, standard deviations Δn and ΔA are in proportion. Possible applications include correlations of the detailed distributions of n and A, three-dimensional foams, and biological tissues.

International audience; When spreading onto a protein microlattice living cells spontaneously acquire simple shapes determined by the lattice geometry. This suggests that, on a lattice, living cells' shapes are in thermodynamic metastable states. Using a model at thermodynamic equilibrium we are able to reproduce the observed shapes. We build a phase diagram based on two adimensional parameters characterizing essential cellular properties involved in spreading: the cell's compressibility and fluctuations.

Differential movement of individual cells within tissues is an important yet poorly understood process in biological development. Here we present a computational study of cell sorting caused by a combination of cell adhesion and chemotaxis, where we assume that all cells respond equally to the chemotactic signal. To capture in our model mesoscopic properties of biological cells, such as their size and deformability, we use the Cellular Potts Model, a multiscale, cell-based Monte Carlo model. We demonstrate a rich array of cell-sorting phenomena, which depend on a combination of mescoscopic cell properties and tissue level constraints. Under the conditions studied, cell sorting is a fast process, which scales linearly with tissue size. We demonstrate the occurrence of “absolute negative mobility”, which means that cells may move in the direction opposite to the applied force (here chemotaxis). Moreover, during the sorting, cells may even reverse the direction of motion. Another interesting phenomenon is “minority sorting”, where the direction of movement does not depend on cell type, but on the frequency of the cell type in the tissue. A special case is the cAMP-wave-driven chemotaxis of Dictyostelium cells, which generates pressure waves that guide the sorting. The mechanisms we describe can easily be overlooked in studies of differential cell movement, hence certain experimental observations may be misinterpreted., Synopsis The movements of biological cells during the development of an organism depend on the physical characteristics of these cells. Genetic regulation of (developmental) cell movements, in order to have an effect, must operate through or in accordance with these physical properties. With this framework in mind, the authors use a computational model to investigate the interaction of two important phenomena, namely differential adhesion and chemotaxis. Authors Käfer, Hogeweg, and Marée show that this interaction leads to fast cell sorting, a process during which the cells actually move in a specific direction, which can even be opposite to the direction of chemotaxis. The direction of motion does not only depend on intrinsic cell properties (such as cell size or the strength of the homotypic and heterotypic bonds) but also on the pattern formation that takes place during the sorting, as well as on general tissue properties. For example, both the formation of cell clusters and the level of confinement of the tissue can completely turn around the direction of sorting. The authors demonstrate that to fully understand cell tissue dynamics, it is essential to take into account mesoscopic cell properties, such as size, shape, and deformability. Because physically driven processes can profoundly influence the movement of biological cells, this should not be neglected in explanations for observed cell movement patterns.

In the plant genus Silene, separate sexes and sex chromosomes are believed to have evolved twice. Silene species that are wholly or largely hermaphroditic are assumed to represent the ancestral state from which dioecy evolved. This assumption is important for choice of outgroup species for inferring the genetic and chromosomal changes involved in the evolution of dioecy, but is mainly based on data from a single locus (ITS). To establish the order of events more clearly, and inform outgroup choice, we therefore carried out (i) multi-nuclear-gene phylogenetic analyses of 14 Silene species (including 7 hermaphrodite or gynodioecious species), representing species from both Silene clades with dioecious members, plus a more distantly related outgroup, and (ii) a BayesTraits character analysis of the evolution of dioecy. We confirm two origins of dioecy within this genus in agreement with recent work on comparing sex chromosomes from both clades with dioecious species. We conclude that sex chromosomes evolved after the origin of Silene and within a clade that includes only S. latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study.

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth–death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations, we illustrate the characteristics of newly proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon diversification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth–death models; extinction; phylogenetics; speciation.]

There is currently a main view describing the steps in the evolution of sex chromosomes in plants in the literature, although alternative views have recently been put forward. First, a non-recombining region (XY or ZW) should emerge. Then, this region is predicted to expand, and at the same time, the local loss of recombination between the sex chromosomes should induce a degeneration of the Y (or W) chromosome. This degeneration is then expected to progress, and after a certain amount of time, the Y (or W) chromosome should become smaller than the X (or Z) chromosome, or even disappear. A main issue of this view is that it is based on the genomic study of only about thirty plant sex chromosome systems, while there are more than 15,000 dioecious species (i.e., plants with separate sexes). As a consequence, while some of these steps are well characterized, others are clearly lacking empirical support. In particular, theformation of a non-recombining region has only been studied theoretically and a strongly degenerated system with a Y (or W) chromosome smaller than the X (or Z) has only been genomically studied in animals. In order to better understand the first step of this view, i.e. the emergence of a non-recombining region, the first part of this thesis focuses on Silene acaulis ssp exscapa, the only subspecies in the Silene acaulis complex that is dioecious. This pattern suggests that dioecy is a recently derived character in this subspecies. Since the sex determination mechanism was unknown in this subspecies, I sought to identify a non-recombining region typical of a pair of sex chromosomes. In order to do so, RNA-seq data was generated from two different populations, to which I applied a new probabilistic tool based on the analysis of genotyping and phenotyping frequencies. This approach allowed me to identify 27 potential XY genes and to propose that they belong to a young sex chromosome system. However, complementary analyses will be required to validate this hypothesis. In order to test whether plants can also present old and strongly degenerated non-recombining regions of sex chromosomes, the second part of this thesis focusses on two dioecious species from the Cannabaceae family, Cannabis sativa et Humulus lupulus. Indeed, these two species diverged 20-25 million years ago and their more recent common ancestor is supposed to be dioecious. Cytological analyses have furthermore shown that sex chromosomes in theses species may be old. To estimate the level of degeneration and the age of this sex chromosome system, I analyzed RNA-seq data generated from one pedigree in each species with a probabilistic tool based on allele segregation patterns. I was able to identify the first sex chromosome system homologous between two genera in plants. This is among the oldest and most degenerated sex chromosome system described in plants so far. Otherwise, detecting Y-specific sequences in these species could improve their crops since only the females are useful and the sexual dimorphism is weak. I designed PCR-primers that showed promising results. Overall, these results shed light on some of the less well-studied steps of the sex chromosome evolution in plants. Indeed, on one hand, we point to a potentially recently emerged system that deserves further attention ; on the other hand, we confirm that old and strongly degenerated sex chromosomes also exist in plants.; La trajectoire décrivant l’évolution d’une paire de chromosomes sexuels à longtemps été proposée comme étant universelle pour tous les systèmes, cependant des propositions alternatives ont récemment nuancé ce «modèle» unique. D’après ce modèle, il y aurait dans un premier temps l’émergence d’une région non-recombinante (XY ou ZW), puis, une expansion de celle-ci. Simultanément, l’absence de recombinaison induit ce que l’on appelle la dégénérescence du chromosome Y (ou W). La dégénérescence est supposée augmenter et, après un certain temps évolutif, devrait conduire à un système dans lequel le chromosome Y (ou W) serait plus petit que le chromosome X (ou Z), voire disparaît. Cependant, seulement une trentaine de paires de chromosomes sexuels de plantes ont été étudiées avec des données empiriques, parmi plus de 15 000 espèces dioïques (i.e. plantes à sexes séparés). Il en résulte que certaines étapes du systèmes sont mieux supportées que d’autres. Plus précisément, la formation de la région non-recombinante a essentiellement été étudiée de manière théorique, tandis qu’une forte dégénérescence avec un chromosome Y (ou W) plus petit que le chromosome X (ou Z) n’a été décrite que chez les animaux. Afin de mieux décrire la première étape du modèle, l’émergence de la région non recombinante, le premier axe de cette thèse représente une étude de Silene acaulis ssp exscapa, la seule sous-espèce dioïque du complexe Silene acaulis. En effet, ceci laisse supposer que ce système sexuel est un caractère dérivé, donc probablement récent. Le mécanisme du déterminisme du sexe n’étant pas connu, j’ai voulu savoir si une région non-recombinante typique d’une paire de chromosomes sexuels est présente chez cette sous-espèce. Pour cela, j’ai utilisé un outil récemment publié basé sur l’analyse de fréquences génotypiques et phénotypiques de mâles et de femelles au sein d’une population. Deux jeux de données RNA-seq provenant de deux populations différentes ont permis d’identifier 27 gènes potentiellement XY, et suggèrent que la paire de chromosomes sexuels serait récente. Des analyses complémentaires sont tout de même nécessaires pour confirmer ces résultats. Deuxièmement, afin de tester l’existence d’une paire ancienne de chromosomes sexuels avec une forte dégénérescence chez les plantes, le deuxième axe de cette thèse est une étude de deux espèces dioïques de la famille des Cannabaceae, Cannabis sativa et Humulus lupulus. En effet, l’ancêtre commun de ces deux espèces, qui divergent depuis plusieurs dizaines de millions d’années, était probablement dioïque. De plus, des analyses cytologiques ont identifié des paires de chromosomes sexuels qui pourraient être anciennes. Pour caractériser l’âge et le niveau de dégénérescence de ces paires de chromosomes sexuels, des données RNA-seq d’un croisement ont été générées pour chacune des deux espèces. Un outil probabiliste analysant les ségrégations alléliques au sein d’un croisement a permis d’identifier la première paire de chromosomes sexuels homologue entre deux genres chez les plantes. De plus, ces chromosomes sexuels sont parmi les plus vieux et les plus dégénérés actuellement décrits chez les plantes. Par ailleurs, la détection de séquence Y-spécifiques pourrait permettre d’améliorer la culture de ces deux espèces puisque seules les femelles ont un intérêt économique et que le dimorphisme sexuel est faible. J’ai développé des amorces PCR qui montrent des résultats prometteurs. Plus généralement, ces résultats apportent de nouvelles informations concernant les étapes les moins bien décrites de l’évolution des chromosomes sexuels chez les plantes. Premièrement, nous montrons qu’une paire de chromosomes sexuels a probablement émergé récemment dans une espèce, et confirmons l’intérêt de continuer à l’étudier. Deuxièmement, nous confirmons que des chromosomes sexuels vieux et fortement dégénérés existent chez les plantes.