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Can speciation occur despite gene flow, and how common is ecological speciation? Crop vulnerability, adaptive introgression, domestication load, genetic incompatibilities, hybrid breakdown, genomic divergence, speciation gene flow, mating system Here, we argue that it also offers an excellent opportunity to catch the very first processes at work in ecological speciation, where adaptive divergence between nascent lineages triggers the onset of reproductive isolation (RI). Keywords: adaptive introgression; crop vulnerability; domestication load; genetic incompatibilities; genomic divergence; hybrid breakdown; mating system; speciation gene flow EN adaptive introgression crop vulnerability domestication load genetic incompatibilities genomic divergence hybrid breakdown mating system speciation gene flow 1 5 5 07/19/23 20230701 NES 230701 BACKGROUND Speciation, Darwin's mystery of mysteries, is a continuous process that results in genomic divergence accompanied by the gradual increment of reproductive barriers between lineages. [Extracted from the article]

Sex-ratio (SR) meiotic drivers are X-linked selfish genetic elements that promote their own transmission by preventing the production of Y-bearing sperm, which usually lowers male fertility. The spread of SR drivers in populations is expected to trigger the evolution of unlinked drive suppressors, a theoretically predicted co-evolution that has been observed in nature. Once completely suppressed, the drivers are expected either to decline if they still affect the fitness of their carriers, or to evolve randomly and possibly get fixed if the suppressors eliminate their deleterious effects. To explore this issue, we used the Paris sex-ratio system of Drosophila simulans in which drive results from the joint effect of two elements on the X chromosome: a segmental duplication and a deficient allele of the HP1D2 gene. We set up six experimental populations starting with 2/3 of X chromosomes carrying both elements (XSR) in a fully suppressing background. We let them evolve independently during almost a hundred generations under strong sexual competition, a condition known to cause the rapid disappearance of unsuppressed Paris XSR in previous experimental populations. In our study, the fate of XSR chromosomes varied among populations, from extinction to their maintenance at a frequency close to the starting one. While the reasons for these variable outcomes are still to be explored, our results show that complete suppression can prevent the demise of an otherwise deleterious XSR chromosome, turning a genetic conflict into cooperation between unlinked loci. Observations in natural populations suggest a contrasting fate of the two elements: disappearance of the duplication and maintenance of deficient HP1D2 alleles. [ABSTRACT FROM AUTHOR]

Background Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. Approaches Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. Conclusions The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution. [ABSTRACT FROM AUTHOR]

Sex chromosome meiotic drive, the non-Mendelian transmission of sex chromosomes, is the expression of an intragenomic conflict that can have extreme evolutionary consequences. However, the molecular bases of such conflicts remain poorly understood. Here, we show that a young and rapidly evolving X-linked heterochromatin protein 1 (HP1) gene, HP1D2, plays a key role in the classical Paris sex-ratio (SR) meiotic drive occurring in Drosophila simulans. Driver HP1D2 alleles prevent the segregation of the Y chromatids during meiosis II, causing female-biased sex ratio in progeny. HP1D2 accumulates on the heterochromatic Y chromosome in male germ cells, strongly suggesting that it controls the segregation of sister chromatids through heterochromatin modification. We show that Paris SR drive is a consequence of dysfunctional HP1D2 alleles that fail to prepare the Y chromosome for meiosis, thus providing evidence that the rapid evolution of genes controlling the heterochromatin structure can be a significant source of intragenomic conflicts. [ABSTRACT FROM AUTHOR]

By distorting Mendelian transmission to their own advantage, X-linked meiotic drive elements can rapidly spread in natural populations, generating a sex-ratio bias. One expected consequence is the triggering of a co-evolutionary arms race between the sex chromosome that carries the distorter and suppressors counteracting its effect. Such an arms race has been theoretically and experimentally established and can have many evolutionary consequences. However, its dynamics in contemporary populations is still poorly documented. Here, we investigate the fate of the young X-linked Paris driver in Drosophila simulans from sub- Saharan Africa to the Middle East. We provide the first example of the early dynamics of distorters and suppressors: we find consistent evidence that the driving chromosomes have been rising in the Middle East during the last decade. In addition, identical haplotypes are at high frequencies around the two co-evolving drive loci in remote populations, implying that the driving X chromosomes share a recent common ancestor and suggesting that East Africa could be the cradle of the Paris driver. The segmental duplication associated with drive presents an unusual structure in West Africa, which could reflect a secondary state of the driver. Together with our previous demonstration of driver decline in the Indian Ocean where suppression is complete, these data provide a unique picture of the complex dynamics of a co-evolutionary arms race currently taking place in natural populations of D. simulans. [ABSTRACT FROM AUTHOR]

Aim To examine mechanisms related to the formation of hybrid zones between the Mediterranean narrow-leaved ash tree Fraxinus angustifolia Vahl and the common ash Fraxinus excelsior L., a mostly temperate tree species, at the continental scale. Location Temperate and Mediterranean Europe and the western part of the Black Sea basin. Methods We used species distribution models to determine the potential zones of sympatry between the two species, which remain largely unknown. In addition, we analysed 58 populations and 456 samples of ash tree that spanned most of the distribution of the two species across Europe, and included both parental species and selected hybrid populations. Levels of hybridization in the 58 populations were estimated using 19 nuclear microsatellite loci, including six anonymous nuclear single sequence repeat ( SSR) markers and 13 recently developed single sequence repeats from expressed RNA sequence tags ( EST- SSRs). Results Bayesian assignment supported the notion of two separate gene pools regardless of the type of marker used, which suggest an ancient population structure. Populations located within the predicted overlap zones had intermediate levels of admixture with a tendency for hybrid populations to occur towards temperate areas. Selection analyses indicated that six of the EST- SSRs had been subjected to stabilizing selection whereas two others had been subjected to directional selection. Results of spatial filtering on the allele frequencies of the loci under directional selection suggest that the number of days of frost and summer temperatures are both ecological factors that can limit the extent of the hybrid zone. Moreover, areas associated with known or predicted hybrid zones showed abrupt changes in allele frequencies compared with the periphery of the distributions. Main conclusions Our analyses suggest that the hybrid structure in these closely related ash species is ancient and asymmetric and that climate-driven selection, in particular cold weather, can potentially limit the extent of hybrid populations. [ABSTRACT FROM AUTHOR]

Intrinsic postzygotic reproductive isolation is thought to result from the substitution of multiple harmless or beneficial genetic differences between species that are incidentally deleterious when combined in species hybrids, causing hybrid sterility or inviability. Genetic variability for hybrid sterility or inviability phenotypes is, however, rarely assessed in natural populations. Here, we assess variation for Drosophila simulans-encoded maternal factor(s) that cause lethality in D. simulans–Drosophila melanogaster F1 hybrid females. First, we survey genetic variability in the strength of D. simulans-mediated maternal effect hybrid lethality among 37 geographic and laboratory isolates. We find abundant variability in the strength of maternal effect hybrid lethality, ranging from complete lethality to none. Second, we assess maternal effect hybrid lethality for a subset of wild isolates made heterozygous with two so-called hybrid rescue strains. The results suggest that the D. simulans maternal effect hybrid lethality involves a diversity of alleles and/or multiple loci. [ABSTRACT FROM PUBLISHER]

One of the greatest challenges of forest restoration is the choice of appropriate plant material that is adapted to local environments, provides the desired ecological services, and does not compromise the local biodiversity. Plant restoration programs use native seeds, a mixture of local and introduced seeds of the same species or allopatric species. However, restoration programs rarely use local hybrid individuals if a local species exhibits natural hybridization. Hybridization is an important evolutionary process that can result in new genotypic combinations that might be suited better to the target habitat than the parental species and allow adaptation to rapid environmental change. European forests are generally under strict legal regulations so that only certified seeds can be used for their restoration. The European certification procedure for seeds from forest trees has been devised to commercialize clearly identified species with known adaptation to a given area. Natural hybrids, for which taxonomic status is uncertain and fitness is generally unknown, are excluded, which is not the case of artificial hybrids because they have been previously tested in the field. Here we discuss the pressing need to include natural hybrid populations as a source of certified seeds for restoration purposes. Using the example of two ash species and their well-adapted hybrids along the Loire River in France, we show why European forest guidelines must be made more flexible to allow the provision of stable ecosystem services. [ABSTRACT FROM AUTHOR]

Segregation Distorter (SD) is a selfish, coadapted gene complex on chromosome 2 of Drosophila melanogaster that strongly distorts Mendelian transmission; heterozygous SD/SD+ males sire almost exclusively SD-bearing progeny. Fifty years of genetic, molecular, and theory work have made SD one of the best-characterized meiotic drive systems, but surprisingly the details of its evolutionary origins and population dynamics remain unclear. Earlier analyses suggested that the SD system arose recently in the Mediterranean basin and then spread to a low, stable equilibrium frequency (1-5%) in most natural populations worldwide. In this report, we show, first, that SD chromosomes occur in populations in sub-Saharan Africa, the ancestral range of D. melanogaster, at a similarly low frequency (∼2%), providing evidence for the robustness of its equilibrium frequency but raising doubts about the Mediterranean-origins hypothesis. Second, our genetic analyses reveal two kinds of SD chromosomes in Africa: inversion-free SD chromosomes with little or no transmission advantage; and an African-endemic inversion-bearing SD chromosome, SD-Mal, with a perfect transmission advantage. Third, our population genetic analyses show that SD-Mal chromosomes swept across the African continent very recently, causing linkage disequilibrium and an absence of variability over 39% of the length of the second chromosome. Thus, despite a seemingly stable equilibrium frequency, SD chromosomes continue to evolve, to compete with one another, or evade suppressors in the genome. [ABSTRACT FROM AUTHOR]