Reproductive Isolation Research Articles

Divergence in Regulatory Regions and Gene Duplications May Underlie Chronobiological Adaptation in Desert Tortoises.

Many cellular processes and organismal behaviours are time-dependent, and asynchrony of these phenomena can facilitate speciation through reinforcement mechanisms. The Mojave and Sonoran desert tortoises (Gopherus agassizii and G. morafkai respectively) reside in adjoining deserts with distinct seasonal rainfall patterns and they exhibit asynchronous winter brumation and reproductive behaviours. We used whole genome sequencing of 21 individuals from the two tortoise species and an outgroup to understand genes potentially underlying these characteristics. Genes within the most diverged 1% of the genome (FST ≥ 0.63) with putatively functional variation showed extensive divergence in regulatory elements, particularly promoter regions. Such genes related to UV nucleotide excision repair, mitonuclear and homeostasis functions. Genes mediating chronobiological (cell cycle, circadian and circannual) processes were also among the most highly diverged regions (e.g., XPA and ZFHX3). Putative promoter variants had significant enrichment of genes related to regulatory machinery (ARC-Mediator complex), suggesting that transcriptional cascades driven by regulatory divergence may underlie the behavioural differences between these species, leading to asynchrony-based prezygotic isolation. Further investigation revealed extensive expansion of respiratory and intestinal mucins (MUC5B and MUC5AC) within Gopherus, particularly G. morafkai. This expansion could be a xeric-adaptation to water retention and/or contribute to differential Mycoplasma agassizii infection rates between the two species, as mucins help clear inhaled dust and bacterial. Overall, results highlight the diverse array of genetic changes underlying divergence, adaptation and reinforcement during speciation.

Patterns of Genomic Heterogeneity in a Classic Field Cricket Mosaic Hybrid Zone

ABSTRACTBarriers to gene exchange can be semi‐permeable; some genes are expected to freely flow across species boundaries whereas others, under divergent selection or responsible for reproductive isolation, might not. Genome scans in recently diverged species have identified divergent genomic regions, a pattern that has often been interpreted as islands of restricted introgression in a background of relatively free gene exchange (“genomic islands of speciation”). Areas of high differentiation, most located in the X chromosome (females XX, males X0), have been identified in the hybridizing field crickets Gryllus firmus and Gryllus pennsylvanicus. These species were assumed to follow an islands of speciation model, with highly differentiated areas interpreted as areas of reduced introgression. We sequenced the G. firmus genome to localize previously studied SNPs and sample a larger area around them in 8 allopatric populations (4 of each species). We use these data to test expectations for the islands model, in which non‐introgressing areas should have both high absolute and relative differentiation. We find that in the allopatric populations, the areas with high relative differentiation (mostly X‐linked), previously interpreted as non‐introgressing, do not have high absolute differentiation as would be expected under the “islands model.” We also show that the estimated divergence time based on nuclear DNA is about 4× older than that estimated based on mtDNA (800 K vs. 200 K years ago). We discuss the implications of our results for introgression into allopatric populations.

Pollinator-mediated isolation promotes coexistence of closely related food-deceptive orchids.

Identifying the factors that contribute to reproductive isolation among closely-related species is key for understanding the diversification of lineages. In this study, we investigate the strength of premating and postmating reproductive isolation barriers between Disa ferruginea and Disa gladioliflora, a pair of closely-related species, often found co-flowering in sympatry. Both species are non-rewarding and rely on mimicry of different rewarding model flowers for attraction of pollinators. We constructed abiotic niche models for different forms of each taxon to measure ecogeographic isolation. Using experimental arrays in sympatry, we recorded pollinator transitions to measure ethological isolation. We performed hand pollinations to measure postpollination isolation. We found strong, but not complete, premating isolation associated with abiotic niches and absolute ethological isolation based on pollinator preferences in sympatry. Pollinator preferences among the orchids could be explained largely by flower colour (orange in D. ferruginea and pink in D. gladioliflora) which matches that of the pollinator food plants. Post-mating barriers were weak as the species were found to be inter-fertile. Coexistence in the orchid species pair is due mainly to ethological reproductive isolation arising from flower colour differences resulting from mimicry of different rewarding plants. These results highlight the importance of signalling traits for ethological isolation of closely-related species with specialized pollination systems.

Postmating prezygotic isolation occurs at two levels of divergence in Drosophila recens and D. subquinaria.

Identifying the presence and strength of reproductive isolating barriers is necessary to understand how species form and then remain distinct in the face of ongoing gene flow. Here we study reproductive isolation at two stages of the speciation process in the closely related mushroom-feeding species Drosophila recens and D. subquinaria. We assess three isolating barriers that occur after mating, including the number of eggs laid, the proportion of eggs laid that hatched, and the number of adult offspring from a single mating. First, all three reproductive barriers are present between D. recens females and D. subquinaria males, which are at the late stages of speciation but still produce fertile daughters through which gene flow can occur. There is no evidence for geographic variation in any of these traits, concurrent with patterns of behavioral isolation. Second, all three of these reproductive barriers are strong between geographically distant conspecific populations of D. subquinaria, which are in the early stages of speciation and show genetic differentiation and asymmetric behavioral discrimination. The reduction in the number of eggs laid is asymmetric, consistent with patterns in behavioral isolation, and suggests the evolution of postmating prezygotic isolation due to cascade reinforcement against mating with D. recens. In summary, not only may postmating prezygotic reproductive barriers help maintain isolation between D. recens and D. subquinaria but they may also drive the earliest stages of isolation within D. subquinaria.

Meiotic Drive and Speciation.

Meiotic drive is the biased transmission of alleles from heterozygotes, contrary to Mendel's laws, and reflects intragenomic conflict rather than organism-level Darwinian selection. Theory has been developed as to how centromeric properties can promote female meiotic drive and how conflict between the X and Y chromosomes in males can promote male meiotic drive. There are empirical data that fit both the centromere drive and sex chromosome drive models. Sex chromosome drive may have relevance to speciation through the buildup of Dobzhansky-Muller incompatibilities involving drive and suppressor systems, studied particularly in Drosophila. Centromere drive may promote fixation of chromosomal rearrangements involving the centromere, and those fixed rearrangements may contribute to reproductive isolation, studied particularly in the house mouse. Genome-wide tests suggest that meiotic drive promotes allele fixation with regularity, and those studying the genomics of speciation need to be aware of the potential impact of such fixations on reproductive isolation. New species can originate in many different ways (including multiple factors acting together), and a substantial body of work on meiotic drive point to it being one of the processes involved.

Genomic and bioacoustic variation in a midwife toad hybrid zone: A role for reinforcement?

Hybrid zones, i.e., geographic areas where diverging lineages meet, hybridize and eventually mix their genomes, offer opportunities to understand the mechanisms behind reproductive isolation and speciation. Hybrid zones are particularly well suited to study reinforcement, i.e., the process by which selection against hybridization increases reproductive barriers, which, in anuran amphibians, is typically expressed by increased divergence in advertisement calls-the main cue to assortative mating-in parapatric ranges. Using mitochondrial barcoding (16S sequences), population genomics (thousands of SNPs) and bioacoustic analyses (four call parameters), we examine the hybrid zone between two incipient species of midwife toads (Alytes obstetricans and A. almogavarii) in southern France, with the purposes of locating their transition, measuring genetic introgression, and documenting potential signatures of reinforcement. We map range boundaries in the Eastern Pyrenees and the southwestern foothills of the Massif Central, namely along the Ariège valley and the Montagne Noire area. Similarly to another transition between these species in Spain, we found the hybrid zone to be narrow, involving geographically restricted gene flow (~20 km wide allele frequency clines) and barrier loci (i.e., loci resisting introgression), both suggestive of partial post-zygotic isolation (hybrid incompatibilities). The calls of the species overlap less inside than outside the hybrid zone, due to a reduction of their standing variation rather than a shift towards distinctive variants. While neutral causes cannot be excluded, this pattern follows the general expectations of reinforcement, yet without reproductive character displacement. Our study highlights the potential of amphibian hybrid zones to assess the genetic and behavioral drivers of reproductive isolation in statu nascendi and under various evolutionary contexts.

Machine Learning Inference of Gene Regulatory Networks in Developing Mimulus Seeds

The angiosperm seed represents a critical evolutionary breakthrough that has been shown to propel the reproductive success and radiation of flowering plants. Seeds promote the rapid diversification of angiosperms by establishing postzygotic reproductive barriers, such as hybrid seed inviability. While prezygotic barriers to reproduction tend to be transient, postzygotic barriers are often permanent and therefore can play a pivotal role in facilitating speciation. This property of the angiosperm seed is exemplified in the Mimulus genus. In order to further the understanding of the gene regulatory mechanisms important in the Mimulus seed, we performed gene regulatory network (GRN) inference analysis by using time-series RNA-seq data from developing hybrid seeds from a viable cross between Mimulus guttatus and Mimulus pardalis. GRN inference has the capacity to identify active regulatory mechanisms in a sample and highlight genes of potential biological importance. In our case, GRN inference also provided the opportunity to uncover active regulatory relationships and generate a reference set of putative gene regulations. We deployed two GRN inference algorithms—RTP-STAR and KBoost—on three different subsets of our transcriptomic dataset. While the two algorithms yielded GRNs with different regulations and topologies when working with the same data subset, there was still significant overlap in the specific gene regulations they inferred, and they both identified potential novel regulatory mechanisms that warrant further investigation.

Different but not isolated: absence of reproductive barriers and strong floral divergence between ecotypes of Epidendrum fulgens (Orchidaceae)

Abstract Reproductive barriers and divergent traits may occur between populations of the same species occurring at different habitat types. Here, we investigated the reproductive compatibility and flower morphology of eight populations of Epidendrum fulgens (Orchidaceae) distributed in two different disjunct environments: coastal sand dunes and inland rock outcrops. We investigated potential reproductive isolation barriers using artificial hand pollination experiments, and considering fruit set and seed viability as proxies for pre- and postzygotic barriers, respectively. For morphology investigation, we analysed the shape of flowers using a geometric morphometric approach. Contrary to our expectations, we found high levels of fruit set (0.85) and seed viability (0.73) in crosses between ecotypes, suggesting a lack of reproductive isolation barriers. Regarding floral morphology, canonical variate analysis revealed all floral parts were significantly different between ecotypes (P < .05), while Procrustes ANOVA on symmetric components of shape indicated lateral sepals (P = .005) and ventral sepal (P = .011) were significantly different. Considering that both ecotypes are found on different habitats, the floral morphological divergence may be affected by specific abiotic conditions affecting flower development and/or different pollinator assemblages. Despite the morphological differences, reproductive barriers between ecotypes are absent, suggesting populations from divergent environments may merge upon secondary contact. Our contrasting results highlight the importance of multidisciplinary approaches for providing insights into the processes operating during the early stages of speciation.

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

BackgroundOver their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential.ResultsWe present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids, Acropora palmata and A. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genus Acropora exhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from one A. palmata family and 16 A. cervicornis families using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM for A. palmata and A. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps.ConclusionsTogether, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the Atlantic Acropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Permeability of postzygotic barriers: embryology of a partially fertile Epidendrum (Orchidaceae) hybrid

Abstract Hybrid zones offer unique insight into reproductive barriers and plant speciation mechanisms. This study investigated postzygotic reproductive isolation in the natural hybrid Epidendrum × purpureum, which occurs in sympatry with its parent species, Epidendrum denticulatum and E. orchidiflorum. We examined the development of male and female gametophytes and the events leading to seed formation in this hybrid zone. Floral buds and flowers from E. × purpureum individuals were collected at various stages of development. Both self‐pollination and backcrosses between hybrids and parental species were performed to follow ovule and seed development up to 60 days after pollination. The material was analysed using optical and confocal microscopy. In most hybrids, microsporogenesis and microgametogenesis occur regularly, forming viable male gametophytes. Non‐viable male gametophytes were also observed and are the result of symmetrical mitotic division. The development of the female gametophyte occurs after self‐pollination, and proceeds regularly, resulting in a reduced female gametophyte. Embryo development in the parental species occurs without abnormalities, while in backcrosses between hybrids and parental species, most embryos degenerate. Embryo degeneration in the crosses between hybrids can be explained by genetic incompatibilities. The co‐occurrence of viable embryos and degenerating embryos in backcrosses between hybrids and parental species point to incomplete postzygotic reproductive barriers between the hybrid and the progenitors. Our findings suggest that E. × purpureum could facilitate gene flow between parental species, as much of its embryological development occurs without abnormalities.

Breeding success of the interspecies hybrids: Reduced fertility in the hybridogeneous magpie population (<i>Pica pica</i> × <i>Pica serica</i>, Aves)

Data on the breeding success of hybrids, collected during direct field observations, are principally important for understanding nature of the species isolating factors and future fate of the hybridogeneous populations. In the zone of secondary contact between Eurasian magpie Pica pica and Oriental magpie Pica serica, emerging right now, limited hybridization occurs, what has been shown in our reported data on nuclear single nucleotide polymorphisms (SNP). In the present work, we have analyzed composition of 119 nesting pairs and content of 89 nests in the hybridogeneous population of P. pica leucoptera × P. serica jankowskii in Eastern Mongolia, then in the recent contact zone in Eastern Transbaikalia (South Siberia) and the relatively pure populations of P. p. leucoptera in Central Transbaikalia and P. s. jankowskii in Northeast China. In the hybridogeneous population of Mongolia, significantly increased portion of nonviable clutches with all dead eggs was recorded, as well as a portion of partly dead clutches, compared with the data on the pure population of Central Transbaikalia. The egg mortality was found to be much less dramatic in the population of the Eastern Transbaikalia, where hybridization is less pronounced than in Mongolia. Several possible mechanisms of genetic incompatibilities breaking the reproductive barriers are discussed. The future fate of this magpie contact zone is considered, taking in account selection against hybridization which was revealed in this study. Among possible scenarios, reinforcement of prezygotic isolation may occur, i. e., in the species-specific calls. It is possible that a kind of mosaic hybrid zone with some features of tension zone will appear. Monitoring of the unique situation with the emerging zone of contact and hybridization of two young magpie species is needed, as a necessary addition to genomic studies.

Genetic species concept as applied to multilocus nuclear data

Using the example of multiple species groups and species complexes, it is empirically shown that the resolving power of a set of 10–20 nuclear loci is insufficient for the study of their genetic differentiation. For the adequate analysis of phylogenetic relationships (including reticulation events) and assessment of divergence levels within such groups of closely related species, it is necessary to multiply the number of nuclear loci and transit to high-throughput next-generation deep sequencing. However, the question of the genomic coverage required for the purposes of such study remains open. In other words, exactly how many genes in a set are needed to measure the genetic distance resolving the relationships between branches on the phylogenetic tree reconstruction of a complex of closely related species? We chose protein-coding sequences as a standard set of markers. Distances for 160–180 genes with a combined length of 270 000–300 000 bp were used to estimate the divergence levels of closely related mammalian species. In most cases, the interspecific distances are within the 0.15–0.75% range (median of 0.33%). The range of distances between semi-species is 0.12–0.28% (median of 0.14%). Intraspecific distances are always lower than 0.11%. Rodents show higher values of interspecific distances, 0.25–2.3% (median of 0.72%); distances between half-species range from 0.1 to 0.35%. To determine the number of nuclear loci and their combined length sufficient for the calculation of a genetic distance, we use simulations based on a model that included the following parameters: the average rate of gene evolution, its dispersion, and the level of polymorphism in the modern and ancestral populations. We performed a preliminary analysis of the distribution of loci evolution rates among mammalian taxa based on the data on ~50 thousand nuclear markers. It is shown that a relative error of 10–15%, comparable to the same value for mitochondrial distances between close species based on individual genes (approximately 1000 bp in length), is achieved using approximately 100 loci of 300 bp in length. Based on these data, we propose the following working hypothesis: the threshold of interspecific/intraspecific genetic distance calculated on the basis of the exons most frequently used in mammalian molecular phylogenetics is approximately 0.15%. This hypothesis assumes a species rank for the forms in statu nascendi. It should be noted that not all “good” species have significant genetic distances, since in some cases reproductive barriers form faster than substitutions accumulate in the genome.

Historical and ongoing hybridisation in Southern South American grassland species

Natural hybridisation in plants can impact genetic and morphological diversity, including the emergence of better-adapted new populations and the potential extinction of some lineages involved in this intricate process. Under progressive global warming, species often need to migrate to newly suitable areas, which may be an additional challenge for species with low dispersal ability. Throughout the search for new environments, previously allopatric lineages can come into secondary contact and eventually hybridise if reproductive isolation is incomplete. Here, we focused on two taxa representing the natural herbaceous component of southern South American lowland grasslands. We aimed to evaluate the impact of contact zones and potential hybridisation on the evolutionary relationships and population dynamics. We used single nucleotide polymorphisms and morphological data of multiple individuals from allopatric and contact zones between taxa to shed light on hybridisation patterns and demographic scenarios. Our results indicated that the contact zones impact taxa’s genetic and morphological diversity, and each contact zone had different patterns of genetic diversity and morphology, constituting stable populations that potentially reflect hybridisation events occurring at distinct evolutionary times.

Reaching people who use drugs with sexual and reproductive healthcare through syringe services programs: potential promise and missed opportunities

BackgroundPeople who use drugs are at elevated sexual and reproductive health risk but experience barriers to services. Syringe services programs (SSP) are an important venue to provide integrated health services. Few studies have examined SSP use within intersecting gender, racial, and ethnic groups, including by injection drug use (IDU), and differences in sexual and reproductive health among these groups.MethodsWithin a cohort study among people who use unprescribed opioids in New York City, we conducted a nested cross-sectional study from November 2021-August 2022 assessing sexual health with a survey (n = 120). The parent study measured baseline characteristics, and the cross-sectional study survey measured self-reported past-year SSP use and sexual and reproductive health. We estimated SSP use within gender, racial, and ethnic groups by IDU, and the prevalence of sexual and reproductive health outcomes by gender, race, ethnicity, and SSP use.ResultsAmong men (n = 61) and women (n = 54), SSP use was disproportionately low among Black participants irrespective of IDU. Women reporting SSP use had a higher prevalence of multiple, new, sex trade, and/or casual sex partners, history of STI symptoms, and lack of effective STI prevention, although women who did not use SSP had non-negligible levels of risk with variation between racial and ethnic groups. Among men, sexual and reproductive health varied across racial and ethnic groups but not as clearly by SSP use.ConclusionsSSP offer opportunity to address elevated STI risk among people who use drugs but may miss certain intersecting gender, race, and ethnic groups.

Impact of Polyploidy on Crop Improvement and Plant Breeding Strategies: A Review

Polyploidy, the condition of possessing multiple sets of chromosomes, is a widespread phenomenon in plants that has had a profound impact on crop evolution and improvement. This review explores the role of polyploidy in plant breeding strategies, emphasizing its contributions to enhancing agronomic traits, overcoming genetic barriers, and expanding genetic diversity. Polyploid crops, such as wheat, cotton, and Brassica species, exhibit superior yield, increased biomass, and enhanced stress tolerance compared to their diploid counterparts. Polyploidy can arise naturally or be induced artificially, providing breeders with opportunities to create novel crop varieties through synthetic polyploidization. The complexity of polyploid genomes poses significant challenges, including fertility issues, meiotic instability, and difficulties in genome management. Advances in genomic and biotechnological tools, such as genomic selection and CRISPR-based genome editing, are beginning to address these obstacles, allowing for precise manipulation of polyploid genomes and improved breeding outcomes. Additionally, polyploidy plays a crucial role in overcoming reproductive barriers in interspecific hybrids, facilitating the transfer of desirable traits between species that would otherwise be genetically incompatible. The potential of polyploidy for developing climate-resilient crops is particularly noteworthy, as polyploid plants often exhibit greater tolerance to drought, salinity, and extreme temperatures. This makes polyploid breeding a promising approach for addressing the challenges of climate change and ensuring food security. Future research should focus on understanding the genetic and epigenetic mechanisms underlying polyploid genome stability and trait expression, as well as integrating advanced computational tools to predict and manipulate polyploid gene function. Emerging areas such as synthetic biology and multi-omics integration will further enhance our ability to engineer polyploid crops with complex trait architectures. Polyploidy remains a powerful and versatile tool for plant breeders, offering immense potential for crop improvement, genetic innovation, and the development of resilient agricultural systems. As the understanding and technological capabilities in polyploid breeding continue to advance, polyploid crops will play a central role in sustainable agricultural development and global food production.

Dosage-sensitive maternal siRNAs determine hybridization success in Capsella.

Hybrid seed failure arising from wide crosses between plant species is a recurring obstacle in plant breeding, impeding the transfer of desirable traits. This postzygotic reproductive barrier primarily occurs in the endosperm, a tissue that nourishes the embryo and functions similarly to the placenta in mammals. We found that incompatible seeds show a loss of DNA methylation and chromatin condensation in the endosperm, similar to seeds lacking maternal RNA polymerase IV activity. This similarity is linked to a decrease in small interfering RNAs in the endosperm (sirenRNAs), maternal RNA polymerase IV-dependent short interfering RNAs that regulate DNA methylation. Several AGAMOUS-like MADS-box transcription factor genes (AGLs), key regulators of endosperm development, are targeted by sirenRNAs in cis and in trans. This finding aligns with the enrichment of AGL target genes among deregulated genes. We propose that hybrid seed failure results from reduced maternal sirenRNAs combined with increased AGL expression, leading to abnormal gene regulation in the endosperm.

Asymmetrical hybridization and environmental factors influence the spatial genetic structure of a killifish hybrid zone.

Hybridization offers insight into speciation and the forces that maintain barriers to reproduction, and hybrid zones provide excellent opportunities to test how environment shapes barriers to reproduction and hybrid fitness. A hybrid zone between the killifish, Fundulus heteroclitus and F. grandis, had been identified in northeastern Florida, although the spatial structure and parameters that affect the distribution of the two species remain unknown. The present study aimed to determine the fine-scale spatial genetic patterns of the hybrid zone to test the hypothesis that species ranges are influenced by changes in dominant vegetation, and to determine how differences in reproductive barriers between the two species influence the observed patterns. The area of overlap between the two species spanned ~37 km and showed a mosaic pattern of hybridization, suggesting the spatial structure of the hybrid zone is largely influenced by the environment. Environmental association analysis, however, suggested that while dominant vegetation had a significant influence on the spatial structure of the hybrid zone, a combination of environmental factors was driving the observed patterns. Hybridization tended to be rare at sites where F. heteroclitus was the more abundant species, suggesting that differences in preference for conspecifics can lead to differences in rates of introgression into parental taxa and likely result in a range-shift as opposed to adaptation in the face of climate change.

A newborn F-box gene blocks gene flow by selectively degrading phosphoglucomutase in species hybrids

The establishment of reproductive barriers such as postzygotic hybrid incompatibility (HI) remains the key to speciation. Gene duplication followed by differential functionalization has long been proposed as a major model underlying HI, but little supporting evidence exists. Here, we demonstrate that a newborn F-box gene, Cni-neib-1, of the nematode Caenorhabditis nigoni specifically inactivates an essential phosphoglucomutase encoded by Cbr-shls-1 in its sister species Caenorhabditis briggsae and their hybrids. Zygotic expression of Cni-neib-1 specifically depletes Cbr-SHLS-1, but not Cni-SHLS-1, in approximately 40 min starting from gastrulation, causing embryonic death. Cni-neib-1 is one of thirty-three paralogues emerging from a recent surge in F-box gene duplication events within C. nigoni, all of which are evolving under positive selection. Cni-neib-1 undergoes turnover even among C. nigoni populations. Differential expansion of F-box genes between the two species could reflect their distinctive innate immune responses. Collectively, we demonstrate how recent duplication of genes involved in protein degradation can cause incidental destruction of targets in hybrids that leads to HI, providing an invaluable insight into mechanisms of speciation.

What Predicts Gene Flow During Speciation? The Relative Roles of Time, Space, Morphology and Climate.

The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Sceloporus) occurring mostly in northeastern Mexico, which show striking variation in morphology and habitat among closely related species and populations. We developed a new time-calibrated phylogeny for the group using RADseq data from 152 individuals. This phylogeny identified 12 putative species-level clades, including at least two undescribed species. We then estimated levels of gene flow among 21 geographically adjacent pairs of species and populations. We also estimated divergence in morphological and climatic niche variables among these same pairs, along with divergence times and geographic distances. Using Bayesian generalised linear models, we found that gene flow between pairs of lineages is negatively related to divergence time and morphological divergence among them (which are uncorrelated), and not to geographic distance or climatic divergence. The framework used here can be applied to study speciation in many other organisms having genomic data but lacking direct data on reproductive isolation. We also found several other intriguing patterns in this system, including the parallel evolution of a strikingly similar montane blue-red morph from more dull-coloured desert ancestors within two different, nonsister species.

A new species of Diacheopsis (Myxomycetes) and a new habitat for myxomycetes

ABSTRACT We describe a new species, Diacheopsis resinae (Myxomycetes), collected from a microhabitat new for myxomycetes: stem wounds of coniferous trees (Norway spruce) where the resin is overgrown with a community of resinicolous fungi. The 80 known collections come from the Vosges (France), the Black Forest (Germany), Swabian Alp (Germany), and several localities in Denmark and Norway. Observations, but as well as metabarcoding of substrate samples with fungal (ITS [internal transcribed spacer]), bacterial (16S rDNA), and myxomycete (18S nuc rDNA) primers from eight trunks, revealed the new myxomycete to co-occur with resin-degrading ascomycetes (Infundichalara microchona, Lophium arboricola, Zythia resinae). The gram-negative bacterial genera Endobacter and Sphingomonas were found to be abundant in the substrate and may be a food source for the myxomycete. Fruit bodies were found mostly during the more humid winter season, with a peak in January/February. Partial sequences of two independent molecular markers (18S nuc rDNA, EF1α [elongation factor 1-alpha] gene) were obtained for 41 accessions, which form a monophyletic cluster in a two-gene phylogeny of Stemonititidales but do not group with other species of Diacheopsis, thus rendering this genus paraphyletic. The new species, although exclusively developing sessile sporocarps and morphologically undoubtedly falling into the genus Diacheopsis, is most closely related to species of Lamproderma, especially L. album, L. zonatum, and L. zonatopulchellum. Within D. resinae, three groups can be differentiated, which show nearly complete reproductive isolation, as judged from a recombination analysis of the two unlinked markers and the allelic combinations of the EF1α gene.