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Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus, R. tiliaster, R. glauciformis, R. slesvicensis and R. firmus

Using flow cytometry and microsatellite DNA analysis (MSDA), we studied hybrids between Rubus caesius and various other Rubus species, with an emphasis on Sweden. We show that hybrids between Rubus caesius and Rubus sect. Corylifolii arise easily. They show a large variation in morphology, but can normally be recognised by a number of characters. They are typically hexaploids, but ~13% of the hybrids are pentaploids and ~8% tetraploids. With MSDA, they are harder to identify than hybrids with R. idaeus, partly because all Corylifolii species have themselves arisen from R. caesius hybrids and therefore share many alleles with R. caesius, partly because hybridisation with R. caesius seems to give rise to some variation in microsatellite regions. Hybrids with species of R. sect. Rubus are much rarer in Sweden and we have only identified one such case. We show that R. cyclomorphus and R. tiliaster are not proper apomictic species, at least not in Sweden, but rather a collection of genetically unrelated hybrids between R. caesius and R. raduloides or R. tiliaster. MSDA analysis of R. slesvicensis and R. firmus shows that these species are problematic. We identify two distinct taxa, one from Skåne in Sweden, which we describe as a new species, R. ruboculus, and another from the neighbourhood of Viborg and Schleswig, although the latter is probably not identical with R. slesvicensis s.s. All the other samples form a diverse group of putative R. caesius hybrids at three different ploidy levels. Rubus glauciformis is uniform in Småland, Öland and Blekinge, but becomes harder to distinguish from various hybrids in Skåne. We conclude that once R. caesius and R. idaeus hybrids are properly identified, along with a small number of new apomictic species (often with a local distribution), the genus Rubus does not pose any serious taxonomical problems in Sweden.

Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas

In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western 'spot-winged tit' (P. a. melanolophus) and eEastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of less than 100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.

Data for: Sigma-B responses of Bacillus subtilis exposed to different environmental stressors and containing different single RsbR proteins or hybrid fusions of RsbRs

Bacteria use a variety of systems to sense stress and mount an appropriate response to assure fitness and survival. Bacillus subtilis uses stressosomes—cytoplasmic multiprotein complexes—to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σB. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σB response profiles with respect to timing and intensity when facing an identical stressor. We used microfluidics and fluorescence microscopy to address the question of whether the σB responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σB with characteristic transient response timing irrespective of stressor but show varying response magnitude. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative and acid stress, implying that RsbR proteins can distinguish among stressors. To show this distinct timing, we quantified time-lapse image series of cells with a fluorescent σB transcriptional reporter. Representative videos of time-lapse image series and the results of our quantitation for each RsbR paralog in each stress condition are included in this dataset. We also probed the relative importance of each half of each RsbR paralog. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argued that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σB response timing. Time-lapse videos for each hybrid fusion protein and the corresponding quantification of these data are also included in the dataset.

Patterns of pollen dispersal and pollen capture in the hybridizing cattails, Typha latifolia and T. angustifolia

Pollen dispersal regulates the formation of the invasive, wind-pollinated hybrid cattail T. × glauca, the F1 offspring of the broadleaf (T. latifolia) and narrowleaf (T. angustifolia cattail. An earlier study suggested that pollen dispersal by T. latifolia might be spatially restricted, with most dispersal occurring over distances less than 2 m. Restricted pollen dispersal would imply that hybrid formation primarily occurs within mixed stands of cattails. Hybrid formation might also be affected by preferential receipt of conspecific pollen, but this has not been investigated for cattails. We compared patterns of pollen dispersal for T. latifolia and T. angustifolia using a wind tunnel. We then tested whether patterns of pollen receipt were biased toward the capture of conspecific versus heterospecific pollen using monospecific cattail stands with a single local pollen source. Results from the wind tunnel partially supported the previous finding of spatially restricted pollen dispersal for T. latifolia, the paternal parent of F1 hybrids. Pollen receipt by T. angustifolia was biased toward the capture of conspecific pollen. Localized pollen dispersal by T. latifolia and preferential conspecific pollen capture by T. angustifolia should reduce rates of hybrid formation below that expected under random mating.

Disturbance-mediated hybridization in black-capped and mountain chickadees

Human habitat disturbances can promote hybridization between closely related, but typically reproductively isolated, species. We explored whether human habitat disturbances are related to hybridization between two closely related songbirds, black-capped, and mountain chickadees, using both genomic and citizen science datasets. First, we genotyped 409 individuals from across both species' ranges using reduced-representation genome sequencing and compared measures of genetic admixture to a composite measure of human landscape disturbance. Then, using eBird observations, we compared human landscape disturbance values for sites where phenotypically diagnosed hybrids were observed to locations where either parental species was observed to determine whether hybrid chickadees are reported in more disturbed areas. We found that hybridization between black-capped and mountain chickadees positively correlates with human habitat disturbances. From genomic data, we found that 1) hybrid index significantly increased with habitat disturbance, 2) more hybrids were sampled in disturbed habitats, 3) mean hybrid indexes were higher in disturbed habitats versus wild habitats, and 4) hybrids were detected in habitats with significantly higher disturbance values than parentals. Using eBird data, we found that both hybrid and black-capped chickadees were significantly more disturbance-associated than mountain chickadees. Surprisingly, we found that nearly every black-capped chickadee we sampled contained some proportion of hybrid ancestry, while we detected very few mountain chickadee backcrosses. Our results highlight that hybridization between black-capped and mountain chickadees is widespread, but initial hybridization is rare (few F1s were detected). We conclude that human habitat disturbances can erode pre-zygotic reproductive barriers between chickadees and that post-zygotic isolation is incomplete. Understanding what becomes of recently hybridizing species following large-scale habitat disturbances is a new, but pressing, consideration for successfully preserving genetic biodiversity in a rapidly changing world.

opencc-zeroDec 2021View details →

Geographic variability of hybridization between red-breasted and red-naped sapsuckers

Hybrid zones reveal the strength of reproductive isolation between populations undergoing speciation and are a key tool in evolutionary biology research. Multiple replicate transects across the same hybrid zone offer insight into the dynamics of hybridization in different environments, clarifying the role of extrinsic forces on the speciation process. Red-breasted and red-naped sapsuckers (Sphyrapicus ruber and S. nuchalis) have a long zone of contact over approximately 1,600 km from central British Columbia, Canada to central California, USA. We used Genotyping-by-Sequencing data from three independent sapsucker hybrid zone transects to compare hybridization dynamics between these species under variable geoclimatic conditions. We generated geographic clines of the genomic data to compare hybrid zone widths and used Random Forest models and linear regression to assess the relationship between climate and sapsucker ancestry along each transect. Our results show variation in the directionality of backcrossing, often indicative of moving hybrid zones. We note variable cline widths among transects, indicating differences in selection maintaining hybrid zone dynamics. Furthermore, Random Forest models identified different variables in close association with sapsucker ancestry across each transect. These results indicate a lack of repeatability across replicate transects and a strong influence of local environment on hybrid zone dynamics.

zenodo36/100

Targeted DNA methylation from cell free DNA using hybrid probe capture

CSV files contain beta value and coverage per base & per region, as indicated in the file name. Columns are samples, rows are CpGs or target region - depending on the file. Files were generated from our bismark/bsseq pipeline as described in the manuscript. Contact: dnbuckle@usc.edu

opencc-by-4.0Jul 2022View details →

zenodo36/100

Dataset for "Harmonic Structure of Lower Hybrid Waves Driven by Energetic Ions at 4000 km Altitude: PIC simulation"

To produce the figures shown in the paper, you can launch Gnuplot and execute the following command: gnuplot> load "(filename).gp" (e.g. load "fig1.gp") For Figs. 1 and 4, you can input the filename in the scripts to produce the figures. For Figs. 2 and 3, you can set a flag variable, flag, as flag=1 to produce the figure in case A or as flag=2 to produce the figure in case B. The label in the plotted figures is the same as in the paper. We prepare CSV files so you can produce the figures with other software.

opencc-by-4.0Nov 2022View details →

Data for: Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.)

When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic barriers, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and Fundulus diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀×H♂). To determine why F. heteroclitus x F. diaphanus F1 hybrids (H♀×D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference, male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, while F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀×D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀×H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀×H♂ crosses had a higher hatching success than F. diaphanus crosses at 10ppt, which may affect their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.

Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and non-target Drosophila species

Genetically engineered gene drives (geGD) are potentially powerful tools for suppressing or even eradicating populations of pest insects. Before living geGD insects can be released into the environment, they must pass an environmental risk assessment (ERA) to ensure that their release will not harm valued and protected entities of the environment. A key research question concerns the likelihood that non-target species will acquire the functional GD elements; such acquisition could lead to the loss of those species and to a disruption of the ecosystem services they provide. The main route for gene flow is through hybridization between the GD insect strain and closely related species that co-occur in the area of release. Using the invasive spotted-wing drosophila, Drosophila suzukii, as a case study, we demonstrate how a combination of interspecific hybridization experiments, behavioral observations, and molecular genetic analyses can be used to assess the potential for hybridization.

Hybrid cline or hybrid lineage: A genomic reevaluation of Sibley's classic species conundrum in Pipilo towhees

Hybrid zones are often described as clines of genetic and phenotypic traits moving across species barriers through introgression. Yet, hybrid zones can also be spatially complex and shift over time, and dispersal and vicariance can isolate portions of a cline, potentially leading to hybrid lineage formation. We reassessed Sibley's (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (P. maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (FST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between hybrid clines and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due both to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. The towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages.

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone

Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine 'top-down' and 'bottom-up' approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of Mimulus aurantiacus. Several candidate isolating traits and anonymous SNP loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline-based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few 'islands of speciation.' Quantitative trait locus (QTL) mapping reveals that most floral traits are polygenic, with little evidence that QTL co-localize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow aside from pollinator isolation may play an important role in this system.

Solidago hybrid-sequence capture probe set

Premise of the study: The phylogenetic relationships among the ca. 138 species of goldenrods (Solidago; Asteraceae) have been difficult to infer due to species richness, and shallow interspecific genetic divergences. This study aims to overcome these obstacles by combining extensive sampling of goldenrod herbarium specimens with the use of a custom Solidago hybrid-sequence capture probe set. Methods: A set of tissues from herbarium samples comprising ca. 90% of Solidago species was assembled, and DNA was extracted. A custom hybrid-sequence capture probe set was designed, and data from 854 nuclear regions were obtained and analyzed from 209 specimens. Maximum likelihood and coalescent approaches were used to estimate the genus phylogeny for 157 diploid samples. Key results: Although DNAs from older specimens were both more fragmented and produced fewer sequencing reads, there was no relationship between specimen age and our ability to obtain sufficient data at the target loci. The Solidago phylogeny was generally well supported, with 88/155 (57%) nodes receiving ≥95% bootstrap support. Solidago was supported as monophyletic, with Chrysoma pauciflosculosa identified as sister. A clade comprising Solidago ericameriodes, Solidago odora, and Solidago chapmanii was identified as the earliest diverging Solidago lineage. The previously segregated genera Brintonia and Oligoneuron were identified as placed well within Solidago. These and other phylogenetic results were used to establish four subgenera and fifteen sections within the genus. Conclusions: The combination of expansive herbarium sampling and hybrid-sequence capture data allowed us to quickly and rigorously establish the evolutionary relationships within this difficult, species-rich group.

opencc-by-4.0Dec 2022View details →

zenodo36/100

Data set for "Electrical spectroscopy of defect states and their hybridization in monolayer MoS2"

Data set for "Electrical spectroscopy of defect states and their hybridization in monolayer MoS2" doi:10.1038/s41467-022-35651-1

Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population

The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise FST-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average HE = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (FIS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (A. brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

On the fast track: Hybrids adapt more rapidly than parental populations in a novel environment

Rates of hybridization are predicted to increase due to climate change and human activity that cause redistribution of species and bring previously isolated populations into contact. At the same time, climate change leads to rapid changes in the environment, requiring populations to adapt rapidly in order to survive. A few empirical cases suggest hybridization can facilitate adaptation despite its potential for incompatibilities and deleterious fitness consequences. Here we use simulations and Fisher's Geometric model to evaluate the conditions and time frame of adaptation via hybridization in both diploids and haplodiploids. We find that hybrids adapt faster to new environments compared to parental populations in nearly all simulated scenarios, generating a fitness advantage that can offset intrinsic incompatibilities and last for tens of generations, regardless of whether the population was diploid or haplodiploid. Our results highlight the creative role of hybridization and suggest that hybridization may help contemporary populations adapt to the changing climate. However, adaptation by hybrids may well happen at the cost of reduced biodiversity, if previously isolated lineages collapse into one.

Hybrid AgNPs/eggshell calcium carbonate particles and their antimicrobial efficiency

In this study, hybrid particles of AgNPs-loaded eggshell calcium carbonate (AgNPs/eCaCO3) were prepared in situ by precipitating the eggshell in the presence of freshly prepared AgNPs with a particle size of 10-30 nm. The hybrid particles were comparatively precipitated in situ at 25 °C and 35 °C using poly (sodium 4-styrenesulphonate) as a polyelectrolyte. The AgNPs/eCaCO3 particles prepared at 25 °C had a spherical morphology with a mean diameter of 3.56 mm, and BET surface area of 85.08 m2/g. On the other hand, the particles prepared at 35 °C had a broader size distribution with a mean diameter of 3.19 mm, and a BET surface area of 79.25 m2/g. AgNPs-loaded commercial calcium carbonate particles (AgNPs/e=CaCO3) comparatively prepared at 35 °C were perfectly spherical with a mean diameter of 5.61 mm. At preparing temperature of 25 °C, the hybrid particles contain AgNPs of 0.78 wt% for AgNPs/eCaCO3 and 3.20 wt% for AgNPs/CaCO3. The AgNPs/eCaCO3 and AgNPs/CaCO3 particles exhibited the same efficiency against bacteria extracted from beef with an average inhibition zone diameter of 7–10 mm according to the modified Kirby–Bauer disc diffusion assay depending on their concentration and beef source. Freshly prepared silver colloids showed comparatively poorer antimicrobial efficiency with an inhibition zone diameter around 7 mm.

Exome sequencing of a hybrid pine species complex on the Qinghai-Tibetan Plateau

This study investigates the evolutionary history of Pinus densata on the Qinghai-Tibetan Plateau (QTP) and genomic heterogeneity across a zone of species transition to understand contemporary dynamics of selection and evolution of species barriers. We analyzed the genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors P. tabuliformis and P. yunnanensis using 40,000 exome probe capture sequencing.

opencc-zeroFeb 2023View details →

Data for: Trinity assembled transcriptome of a Eurasian (Myriophyllum spicatum) and a hybrid (M. spicatum × M. sibiricum) genotype of watermilfoil

Aquatic plant managers frequently treat Eurasian watermilfoil (Myriophyllum spicatum L.; EWM) and hybrid watermilfoil (Myriophyllum spicatum L. × Myriophyllum sibiricum Komarov) with 2,4-dichlorophenoxyacetic acid (2,4-D) herbicide. However, watermilfoil genotypes can differ in their response to 2,4-D. In this study, we compared facultative and constitutive gene expression differences for two watermilfoil genotypes (one Eurasian and one hybrid) that differ in their sensitivity to 2,4-D. To do this, we compared between control and 0.5mg L-1 2,4-D treated plants at four time points after treatment. We also assembled the first de novo watermilfoil transcriptome. We found that while qualitatively similar, the facultative transcriptional response of the EWM genotype to 2,4-D treatment was much stronger than the hybrid genotype, indicated by a greater number and log-fold-change of differentially expressed genes at all time points after treatment. Further, we found that the EWM and hybrid genotype differed in their 9-cis-epoxycarotenoid dioxygenase (NCED) and abscisic acid (ABA) gene response, and that there was a greater amount of photosynthesis gene downregulation (both in number and log-fold-change) in the EWM than the hybrid genotype. At the constitutive level, overall, the hybrid expressed genes at a higher level than the EWM genotype, but not the genes of the 2,4-D response pathway. These differences in gene expression match with the degree of phenotypic difference in growth observed between these genotypes when exposed to 2,4-D. The hybrid genotype used here mitigates the effects of 2,4-D treatment better than the EWM genotype at both the molecular and phenotypic level. More study is needed to understand the mechanism(s) of mitigation and whether this is a cause of hybridity, or the specific genotypic backgrounds used here.