Studying patterns of intra-specific genetic variation among populations allows for a better understanding of population structure and local adaptation. However, those patterns may differ according to ...the genetic markers applied, as neutral genetic markers reflect demographic processes and random genetic drift, whereas adaptive markers also carry the footprint of selection. In combination, neutral and adaptive genetic markers permit to assess the relative roles of drift and selection in shaping population structure. Among the best understood adaptive genetic loci are the genes of the major histocompatibility complex (MHC). We here study variation and differentiation at neutral SNP markers and MHC class II genes in red grouse (Lagopus lagopus scotica) from Ireland and Scotland. Irish red grouse populations are fragmented and drastically declining, but red grouse are abundant in Scotland. We find evidence for positive selection acting on the MHC genes and variation in MHC gene copy numbers among Irish individuals. Furthermore, there was significant population differentiation among red grouse from Ireland and Scotland at the neutral SNP markers (FST = 0.084) and the MHC-BLB genes (FST: BLB1 = 0.116, BLB2 = 0.090, BLB3 = 0.104). Differentiation at the MHC-BLB1 was significantly higher than at the neutral SNP markers, suggesting that selection plays an important role in shaping MHC variation, in addition to genetic drift. We speculate that the observed differentiation pattern might be due to local adaptation to different parasite regimes. These findings have strong conservation implications and we advise against the introduction of Scottish red grouse to supplement Irish populations.
The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. ...Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.
Infectious diseases are causing catastrophic losses to global biodiversity. Iridoviruses in the genus
Ranavirus
are among the leading causes of amphibian disease-related mortality. Polymorphisms in ...major histocompatibility complex (MHC) genes are significantly associated with variation in amphibian pathogen susceptibility. MHC genes encode two classes of polymorphic cell-surface molecules that can recognize and bind to diverse pathogen peptides. While MHC class I genes are the classic mediators of viral-acquired immunity, larval amphibians do not express them. Consequently, MHC class II gene diversity may be an important predictor of
Ranavirus
susceptibility in larval amphibians, the life stage most susceptible to
Ranavirus
. We surveyed natural populations of larval wood frogs (
Rana sylvatica
), which are highly susceptible to
Ranavirus
, across 17 ponds and 2 years in Maryland, USA. We sequenced the peptide-binding region of an expressed MHC class IIβ locus and assessed allelic and genetic diversity. We converted alleles to functional supertypes and determined if supertypes or alleles influenced host responses to
Ranavirus
. Among 381 sampled individuals, 26% were infected with
Ranavirus
. We recovered 20 unique MHC class IIβ alleles that fell into two deeply diverged clades and seven supertypes. MHC genotypes were associated with
Ranavirus
infection intensity, but not prevalence. Specifically, MHC heterozygotes and supertype ST1/ST7 had significantly lower
Ranavirus
infection intensity compared to homozygotes and other supertypes. We conclude that MHC class IIβ functional genetic variation is an important component of
Ranavirus
susceptibility. Identifying immunogenetic signatures linked to variation in disease susceptibility can inform mitigation strategies for combatting global amphibian declines.
Species with narrow environmental tolerances are often distributed within fragmented patches of suitable habitat, and dispersal among these subpopulations can be difficult to directly observe. ...Genetic data can help quantify gene flow between localities, which is especially important for vulnerable species with a disjunct range. The Shenandoah salamander (Plethodon shenandoah) is a federally endangered species known only from three mountaintops in Virginia, USA. To reconstruct the evolutionary history and population connectivity of this species, we generated both mitochondrial and nuclear data using sequence capture from individuals collected across all three mountaintops. Applying population and landscape genetic methods, we found strong population structure that was independent of geographic distance. Both the nuclear markers and mitochondrial genomes indicated a deep split between the most southern population and the genetically similar central and northern populations. Although there was some mitochondrial haplotype‐splitting between the central and northern populations, there was admixture in nuclear markers. This is indicative of either a recent split or current male‐biased dispersal among mountain isolates. Models of landscape resistance found that dispersal across north‐facing slopes at mid‐elevation levels best explain the observed genetic structure among populations. These unexpected results highlight the importance of incorporating landscape features in understanding and predicting the movement and fragmentation of this range‐restricted salamander species across space.
The endangered salamander Plethodon shenandoah has an extremely narrow and fragmented range that is limited to three, approximately equidistant, mountaintops. Nuclear and mitochondrial DNA sequence data show that two populations are admixed and exhibit male‐biased gene flow, whereas the third population is completely isolated. Landscape genetic analyses found that dispersal is likely restricted to north‐facing slopes at intermediate elevations.
In occupancy studies, species misidentification can lead to false‐positive detections, which can cause severe estimator biases. Currently, all models that account for false‐positive errors only ...consider omnibus sources of false detections and are limited to single‐species occupancy.
However, false detections for a given species often occur because of the misidentification with another, closely related species. To exploit this explicit source of false‐positive detection error, we develop a two‐species occupancy model that accounts for misidentifications between two species of interest. As with other false‐positive models, identifiability is greatly improved by the availability of unambiguous detections at a subset of site x occasions. Here, we consider the case where some of the field observations can be confirmed using laboratory or other independent identification methods (“confirmatory data”).
We performed three simulation studies to (1) assess the model's performance under various realistic scenarios, (2) investigate the influence of the proportion of confirmatory data on estimator accuracy and (3) compare the performance of this two‐species model with that of the single‐species false‐positive model. The model shows good performance under all scenarios, even when only small proportions of detections are confirmed (e.g. 5%). It also clearly outperforms the single‐species model.
We illustrate application of this model using a 4‐year dataset on two sympatric species of lungless salamanders: the US federally endangered Shenandoah salamander Plethodon shenandoah, and its presumed competitor, the red‐backed salamander Plethodon cinereus. Occupancy of red‐backed salamanders appeared very stable across the 4 years of study, whereas the Shenandoah salamander displayed substantial turnover in occupancy of forest habitats among years.
Given the extent of species misidentification issues in occupancy studies, this modelling approach should help improve the reliability of estimates of species distribution, which is the goal of many studies and monitoring programmes. Further developments, to account for different forms of state uncertainty, can be readily undertaken under our general approach.
The complete mitochondrial genome of Salamandra salamandra was reconstructed using bycatch sequences from an RNAseq library generated from muscle tissue. This study shows the potential of using data ...originally produced for transcriptome assembly to additionally generate complete mitochondrial genomes. The resulting mitogenome was circular, consisted of 16,331 bp and followed the standard vertebrate gene order. Subsequent analysis of the current mitochondrial genome sequence for the species as listed on GenBank highlighted a species misidentification.
In polygynous lizards, male–male competition is an important driver of morphologic and behavioral traits associated with intraspecific dominance. The extent to which females engage in aggressive ...behavior and thus contribute to competition-driven morphologic variation is not well studied. We used injury frequencies of brown anoles (Anolis sagrei) in 16 island populations to test the hypothesis that injury-inducing aggressive encounters increase with population density in both male and female lizards. We further asked whether intraspecific competition is a potential driver of phenotypic traits related to dominance by using population density as proxy for intraspecific competition. We found that the proportion of individuals with injuries was greater in populations with higher densities, suggesting that agonistic competitive interactions increase with population density. Size-adjusted head length of male and female lizards increased with population density, suggesting that larger heads might be advantageous when intraspecific competition is strong. We detected differences in morphology and injury frequency among islands for both males and females, which suggests that agonistic competitive interactions among females may be stronger than previously appreciated. Further research is needed to determine whether aggressive encounters involving females are restricted to intrasexual competition or whether they also involve males, and how morphologic traits of females are related to competitive dominance and reproductive success.
The NOvA experiment is a long-baseline neutrino oscillation experiment. Consisting of two functionally identical detectors situated off-axis in Fermilab's NuMI neutrino beam. The Near Detector ...observes the unoscillated beam at Fermilab, while the Far Detector observes the oscillated beam 810 km away. This allows for measurements of the oscillation probabilities for multiple oscillation channels, ν_µ → ν_µ, anti ν_µ → anti ν_µ, ν_µ → ν_e and anti ν_µ → anti ν_e, leading to measurements of the neutrino oscillation parameters, sinθ_23, ∆m^2_32 and δ_CP. These measurements are produced from an extensive analysis of the recorded data. Deep neural networks are deployed at multiple stages of this analysis. The Event CVN network is deployed for the purposes of identifying and classifying the interaction types of selected neutrino events. The effects of systematic uncertainties present in the measurements on the network performance are investigated and are found to cause negligible variations. The robustness of these network trainings is therefore demonstrated which further justifies their current usage in the analysis beyond the standard validation. The effects on the network performance for larger systematic alterations to the training datasets beyond the systematic uncertainties, such as an exchange of the neutrino event generators, are investigated. The differences in network performance corresponding to the introduced variations are found to be minimal. Domain adaptation techniques are implemented in the AdCVN framework. These methods are deployed for the purpose of improving the Event CVN robustness for scenarios with systematic variations in the underlying data.
Display omitted
•15 Bufotes species dissected by genomics and multiple genetic/biometric datasets.•Widespread mitochondrial replacements and the super-cryptic species concept.•Diverse but asymmetric ...origins of allopolyploid hybrid species.•A discontinuous speciation continuum across 10 pairs of hybridizing lineages.•Major taxonomic revisions, including the descriptions of two new species.
The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopolyploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (<6My), above which species barely admix and eventually evolve different mating calls (6–10My), or can successfully cross-breed through allopolyploidization (>15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians.
Macrophages are involved in immune defense, organogenesis and tissue homeostasis. Macrophages contribute to the different phases of mammary gland remodeling during development, pregnancy and ...involution postlactation. Less is known about the dynamics of mammary gland macrophages in the lactation stage. Here, we describe a macrophage population present during lactation in mice. By multiparameter flow cytometry and single-cell RNA sequencing, we identified a lactation-induced CD11c
CX3CR1
Dectin-1
macrophage population (liMac) that was distinct from the two resident F4/80
and F4/80
macrophage subsets present pregestationally. LiMacs were predominantly monocyte-derived and expanded by proliferation in situ concomitant with nursing. LiMacs developed independently of IL-34, but required CSF-1 signaling and were partly microbiota-dependent. Locally, they resided adjacent to the basal cells of the alveoli and extravasated into the milk. We found several macrophage subsets in human milk that resembled liMacs. Collectively, these findings reveal the emergence of unique macrophages in the mammary gland and milk during lactation.
PDF
