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Selfish genetic elements contribute to hybrid incompatibility and bias or drive their own transmission1,2. Chromosomal drive typically functions in asymmetric female meiosis, whereas gene drive is normally post-meiotic and typically found in males. Here, using single-molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Z. mays ssp. mexicana) that depends on RNA interference (RNAi). 22-nucleotide small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1 and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas3, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize4. A survey of maize traditional varieties and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least four chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive probably had a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of self small RNAs in the germ lines of plants and animals.

ABSTRACT Ungulates serve as the primary carrion source for facultative scavengers in European ecosystems. In the absence of large carnivores, such as wolves (Canis lupus), human hunting leftovers are the main source of carrion for these scavengers. Additionally, wild boars (Sus scrofa) are heavily culled in many ecosystems and are both a significant prey species for wolves as well as a key scavenger. Nowadays, wolves and wild boars are re‐establishing their historical home ranges. However, it remains unclear how their presence influences the population dynamics of facultative scavengers under different scenarios of human hunting strategies. We simulated the biomass densities of all states in the trophic web including European scavengers and wolves using an ordinary differential equations (ODE) model. The presence of wolves led to a positive trend in scavenger biomass in general. However, in general, we found that plant‐based resources were more important for scavenger dynamics than carrion, regardless of whether the carrion originated from human hunting or wolf predation. Only when wolves were absent but boars present, the human hunting strategy became important in determining scavenger dynamics via carrion supply. In conclusion, our model indicates that population dynamics of facultative scavengers are not mainly driven by the availability of carrion, but rather by the presence of and competition for vegetation. Furthermore, our simulations highlight the importance of adapting human hunting strategies in accordance with the re‐establishment of wolf and boar as these can cause fluctuating population patterns over the years.

ABSTRACT Recent advances in sequencing methods have greatly expanded the knowledge of teleost-associated microorganisms. While fish-gut microbiomes are comparatively well studied, less attention has gone toward other, external organ-microbiome associations. Gills are particularly interesting to investigate due to their functions in gas exchange, osmoregulation, and nitrogen excretion. We recently discovered a branchial symbiosis between nitrogen-cycling bacteria and teleosts (zebrafish and carp), in which ammonia-oxidizing Nitrosomonas and denitrifying bacteria together convert toxic ammonia excreted by the fish into harmless dinitrogen (N2) gas. This symbiosis can function as a “natural biofilter” in fish gills and can potentially occur in all ammonotelic fish species, but it remains unknown how widespread this symbiosis is. In this study, we analyzed all publicly available gill microbiome data sets and checked for the presence of Nitrosomonas. We discovered that more than half of the described fish gill microbiomes contain 16S rRNA gene sequences of ammonia-oxidizing bacteria (AOB). The presence of gill-specific AOB was shown in both wild and aquacultured fish, as well as in marine and freshwater fish species. Based on these findings, we propose that ammonia oxidizers are widespread in teleost fish gills. These gill-associated AOB can significantly affect fish nitrogen excretion, and the widespread nature of this association suggests that the gill-associated AOB can have similar impacts on more fish species. Future research should address the contribution of these microorganisms to fish nitrogen metabolism and the fundamental characteristics of this novel symbiosis.IMPORTANCERecent advances in sequencing have increased our knowledge of teleost-associated microbiota, but the gill microbiome has received comparatively little attention. We recently discovered a consortium of nitrogen-cycling bacteria in the gills of common carp and zebrafish, which are able to convert (toxic) ammonia into harmless dinitrogen gas. These microorganisms thus function as a natural nitrogen biofilter. We analyzed all available gill microbiome data sets to determine how widespread gill-associated ammonia-oxidizing bacteria (AOB) are. More than half of the data sets contained AOB, representing both aquacultured and wild fish from freshwater and marine habitats. In total, 182 amplicon sequencing variants were obtained, of which 115 were found specifically in the gills and not the environmental microbiomes. As gill-associated AOB are apparently widespread in teleost fish, it is important to study their impact on host nitrogen excretion and the potential to reduce ammonia accumulation in (recirculating) aquaculture of relevant fish species.

Abstract Scavenging mammals and vultures can exploit and deplete carcasses much faster than other birds and invertebrates. Vultures are strongly influenced by habitat type, e.g. tree cover, since they rely on their eyesight to detect carcasses. It remains unclear whether and how facultative scavengers – both other birds and mammals – are influenced by tree cover and how that affect carcass decomposition time, which in turn affects biodiversity and ecological processes, including the cycle of energy and nutrients. We studied whether the carcass detection and consumption, hence carcass decomposition speed, by facultative avian and mammalian scavengers varies with tree cover in areas without vultures. Fresh mammal carcasses were placed in different landscapes across the Netherlands at locations that widely varied in tree cover. Camera traps were used to record carcass exploitation by facultative avian and mammalian scavengers and to estimate carcass decomposition time. We found that carcass detection and consumption by birds, wild boar, and other mammals varied between locations. Carcass decomposition speed indeed increased with carcass detection and exploitation by mammals, especially by wild boar. However, this variation was not related to tree cover. We conclude that tree cover is not a major determinant of carcass exploitation by facultative scavengers in areas without obligate scavengers and large carnivores.

Continuous nitrogen deposition threatens ecosystems by acidifying soils, causing a stoichiometric imbalance in the vegetation and ultimately, the disappearance of plant and animal species. There is a gap in knowledge of how decomposers such as oribatid mites cope with the effects of nitrogen deposition. Therefore, we conducted feeding experiments with the herbivorous mite Platynothrus peltifer (C.L. Koch, 1839) to assess its fitness as a measure of its reproductive response towards different nitrogen levels in its diet. Mites were collected from the field, starved, and allowed to lay eggs. We recorded the number of eggs during 60 days of experimental trial. The fecundity of mites varied with different elemental compositions, whereby phosphorus seemed to be a limiting factor. With ongoing nitrogen deposition in the future and concomitant phosphorus limitation, we expect a negative impact on the population dynamics of herbivorous decomposers such as Platynothrus peltifer.

Investigators have recently introduced powerful methods for population genetic inference that rely on supervised machine learning from simulated data. Despite their performance advantages, these methods can fail when the simulated training data does not adequately resemble data from the real world. Here, we show that this "simulation mis-specification" problem can be framed as a "domain adaptation" problem, where a model learned from one data distribution is applied to a dataset drawn from a different distribution. By applying an established domain-adaptation technique based on a gradient reversal layer (GRL), originally introduced for image classification, we show that the effects of simulation mis-specification can be substantially mitigated. We focus our analysis on two state-of-the-art deep-learning population genetic methods-SIA, which infers positive selection from features of the ancestral recombination graph (ARG), and ReLERNN, which infers recombination rates from genotype matrices. In the case of SIA, the domain adaptive framework also compensates for ARG inference error. Using the domain-adaptive SIA (dadaSIA) model, we estimate improved selection coefficients at selected loci in the 1000 Genomes CEU population. We anticipate that domain adaptation will prove to be widely applicable in the growing use of supervised machine learning in population genetics.

The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.

Previous work has investigated selection in the coding genome, but it is not as well characterized in the non-coding genome. By analyzing rare variants in 70k genome sequences from gnomAD, the authors detect very strong purifying selection ("ultraselection”) across the human genome, finding it in some microRNAs and coding sequences but generally rare in regulatory sequences.

Increased nitrogen and acidifying deposition negatively affect biogeochemical cycles and nutrient stoichiometry, particularly in oligotrophic habitats. In heathlands, management aims to mitigate effects of deposition by topsoil removal (sod‐cutting) or by liming to increase soil pH. However, these management efforts may further exacerbate macro‐ and micronutrient stoichiometric mismatch, with cascading effects on heathland insects.Here, we investigate the physiological mechanisms by which deposition and management affect insects, focusing on nutrient uptake and excretion. We combined a phosphorus (P) addition and liming experiment in previously sod‐cut heathland with laboratory‐rearing experiments using the field cricket (Gryllus campestris L., 1) as a model species. We hypothesized that P addition would benefit cricket performance by reducing food N:P ratio. Conversely, we hypothesized that liming would reduce performance by decreasing food Mn:Mg and/or Fe:Mg ratios.Elemental uptake efficiency, consumption and reproduction, as well as cricket field density, were significantly higher under increased P availability, confirming insect P limitation in the field. Liming decreased food Mn:Mg ratio and reduced reproductive success, eliminating any beneficial effects of P addition. Moreover, cricket stoichiometry better explained growth rates than the amount of food consumed. The best model highlighted cricket N and Mn content, with increasing N content negatively influencing growth, while the opposite was true for Mn. We found no support for liming‐induced Fe limitation.We propose that both P and Mn limit crickets independently. Specifically, P limitation affects growth via reduced ribosomal content, and Mn limitation impacts growth by limiting arginase activity and hence restricting the recycling of amino acids.Our study shows that restoration management can fail to restore habitat quality for insects and may even amplify mismatches in macro and micronutrient stoichiometry. To address this, the addition of not only P but also Mn may be required as follow‐up management, but reducing N‐emission remains imperative as this removes the need for disruptive management interventions. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Ammonia accumulation is a major challenge in intensive aquaculture, where fish are fed protein-rich diets in large rations, resulting in increased ammonia production when amino acids are metabolized as energy source. Ammonia is primarily excreted via the gills, which have been found to harbor nitrogen-cycle bacteria that convert ammonia into dinitrogen gas (N2) and therefore present a potential in situ detoxifying mechanism. Here, we determined the impact of feeding strategies (demand-feeding and batch-feeding) with two dietary protein levels on growth, nitrogen excretion, and nitrogen metabolism in common carp (Cyprinus carpio, L.) in a 3-week feeding experiment. Demand-fed fish exhibited significantly higher growth rates, though with lower feed efficiency. When corrected for feed intake, nitrogen excretion was not impacted by feeding strategy or dietary protein, but demand-fed fish had significantly more nitrogen unaccounted for in the nitrogen balance and less retained nitrogen. N2 production of individual fish was measured in all experimental groups, and production rates were in the same order of magnitude as the amount of nitrogen unaccounted for, thus potentially explaining the missing nitrogen in the balance. N2 production by carp was also observed when groups of fish were kept in metabolic chambers. Demand feeding furthermore caused a significant increase in hepatic glutamate dehydrogenase activities, indicating elevated ammonia production. However, branchial ammonia transporter expression levels in these animals were stable or decreased. Together, our results suggest that feeding strategy impacts fish growth and nitrogen metabolism, and that conversion of ammonia to N2 by nitrogen cycle bacteria in the gills may explain the unaccounted nitrogen in the balance.

Highways can fragment habitat and be a significant mortality source for mammals. Wildlife exclusion fencing has been shown to reduce wildlife-vehicle collisions, but can also prevent animals from escaping the highway corridor if they enter at access roads or at fence ends. Earthen escape ramps, or “jumpouts,” have been proposed as a possible solution but remain relatively untested. From 2012-2014, we used wildlife cameras to continuously document wildlife use of four jumpout ramps constructed as part of a 2.5-mile wildlife exclusion fence project along Highway 101 near San Luis Obispo, California. Mule deer occasionally used the jumpouts, but quantifying the rate of utilization was confounded by repeated visits by the same individuals. Male and female deer appeared to have different responses to the jumpouts, which warrants deeper investigation using additional data collected from further monitoring through mid-2017. The longer dataset will also better document how individual deer learn to use the jumpouts. Fenced highways can also reduce connectivity unless there is sufficient use of crossing structures. We documented mountain lion, bobcat, black bear, and mule deer used culverts and underpasses in and adjacent to the wildlife fence zone from 2012-2014. Mule deer used the large underpasses almost exclusively, and rarely if ever used culverts. Bear used a wider variety of structures, and bobcats were detected at almost every site and at a higher rate than the other taxa. Mountain lion detections were quite rare, likely due to lower population density in the study area. We propose a deeper multivariate analysis of the factors influencing these species’ use of culverts including culvert dimensionality, nearby habitat, and proximity to cover, based on an expanded dataset of up to five years of continual monitoring at certain sites. The goal of these analyses is to provide information that will help reduce wildlife-vehicle collisions while facilitating regional wildlife connectivity.

Abstract High-throughput CRISPR-Cas9 knockout screens are widely used to evaluate gene essentiality in cancer research. Here we introduce a probabilistic modeling framework, Analysis of CRISPR-based Essentiality (ACE), that accounts for multiple sources of variation in CRISPR-Cas9 screens and enables new statistical tests for essentiality. We show using simulations that ACE is effective at predicting both absolute and differential essentiality. When applied to publicly available data, ACE identifies known and novel candidates for genotype-specific essentiality, including RNA m6-A methyltransferases that exhibit enhanced essentiality in the presence of inactivating TP53 mutations. ACE provides a robust framework for identifying genes responsive to subtype-specific therapeutic targeting.

Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (Monarcha castaneiventris) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira M. c. megarhynchus has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA/SC) M. c. ugiensis is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the MC1R pigmentation gene are associated with melanism on SA/SC, while ASIP, an antagonistic ligand of MC1R, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. MC1R shows evidence of a recent, strong, soft selective sweep. The region including ASIP shows more complex signatures; however, we find evidence for sweeps in mutations near ASIP, which are comparatively older than those on MC1R and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies. Author summary Chestnut-bellied Monarchs (Monarcha castaneiventris ugiensis) from two archipelagos in the Solomon Islands have evolved entirely black plumage from a chestnut ancestor (Monarcha castaneiventris megarhynchus), a phenomenon known as island melanism. We obtain and analyze whole genome sequences using traditional summary statistics and new methods that combine inference of the ancestral recombination graph with machine learning. We find multiple lines of evidence for independent selective sweeps on the MC1R and ASIP genes, a receptor/ligand pair which regulates the production of melanin. Melanism on each archipelago is mediated by mutations in one of these two genes. Mutations in and around MC1R underwent a recent soft sweep experiencing strong selection on the islands of Santa Ana and Santa Catalina, whereas selection was also strong but comparatively older for ASIP on the island of Ugi. We show how melanism originated under positive selection on independent molecular targets, evolving convergently in taxa where coloration mediates reproductive isolation.

Ungulates serve as the primary carrion source for facultative scavengers in European ecosystems. In the absence of large carnivores, such as wolves (Canis lupus), human hunting leftovers are the main source of carrion for these scavengers. Additionally, wild boars (Sus scrofa) are heavily culled in many ecosystems and are both a significant prey species for wolves as well as a key scavenger. Nowadays, wolves and wild boars are re‐establishing their historical home ranges. However, it remains unclear how their presence influences the population dynamics of facultative scavengers under different scenarios of human hunting strategies. We simulated the biomass densities of all states in the trophic web including European scavengers and wolves using an ordinary differential equations (ODE) model. The presence of wolves led to a positive trend in scavenger biomass in general. However, in general, we found that plant‐based resources were more important for scavenger dynamics than carrion, regardless of whether the carrion originated from human hunting or wolf predation. Only when wolves were absent but boars present, the human hunting strategy became important in determining scavenger dynamics via carrion supply. In conclusion, our model indicates that population dynamics of facultative scavengers are not mainly driven by the availability of carrion, but rather by the presence of and competition for vegetation. Furthermore, our simulations highlight the importance of adapting human hunting strategies in accordance with the re‐establishment of wolf and boar as these can cause fluctuating population patterns over the years. [ABSTRACT FROM AUTHOR]

Two new mite species belonging to the genus Stereotydeus Berlese, 1901 were discovered from locations along the coast of Victoria Land, continental Antarctica. Previous records of this genus in the area under study only reported the presence of S. belli and S. mollis. Although those studies included no morphological analyses, it has since been assumed that only these species were present within the area. Specimens of S. ineffabilis sp. nov. and S. nunatakis sp. nov. were obtained, sometimes in sympatry, from four different localities in Central and South Victoria Land and are here described and illustrated using optical and scanning electron microscopy (SEM) techniques. Features useful for identification of the two new Stereotydeus species include the size of the specimens, the length of the apical segment of pedipalps, the presence/absence of division of the femora, the position of solenidia, the shape and disposition of the rhagidiform organs on the tarsi, the shape of the apical setae of the tarsi, the numbers of aggenital setae and the position of the anal opening. A key to 14 of the 15 currently described Antarctic and sub-Antarctic Stereotydeus species is provided.

Abstract Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) to allow practical and sensitive multiple alignment of diverged plant genomes and calculation of conservation scores with minimal user inputs. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the effect of different masking approaches and parameters of the LAST aligner using genome assemblies of 33 grass species. Compared with conventional masking with RepeatMasker, a masking approach based on k‐mers (nucleotide sequences of k length) increased the alignment rate of coding sequence and noncoding functional regions by 25 and 14%, respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for noncoding functional regions by over 52% compared with default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of noncoding sites that can be scored for conservation by over 76%. Overall, tuning of masking and alignment parameters can generate optimized multiple alignments to drive biological discovery in plants.