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Foleshill Friends: George Eliot and Mary Sibree Cash
No full textArticle from the George Eliot Review. Digitized and hosted by the George Eliot Review Online, editor Beverley Park Rilett.Publishe
Data for: Genome assembly, annotation, and SNP discovery of the blackstripe livebearer Poeciliopsis prolifica shed light on fish placenta evolution
No full textPoeciliidae is a family of live-bearing fish in which some species fully provision eggs before fertilization (lecithotrophy) and some continue to provision embryos after fertilization (matrotrophy). The viviparous matrotrophic species have evolved a structure with functional similarity to the mammalian placenta. In placental mammals, the evolutionary innovation of placenta led to parental conflict, resulting in a phenomenon known as genomic imprinting. To investigate potential genome imprinting in placental fish, crosses from inbred lines are needed to track the parental allele transmission directions to estimate allele-specific expression. In this study, we developed two inbred lines of blackstripe livebearer Poeciliopsis prolifica, a placental Poeciliid whose embryos increase in dry mass by a factor of 7 during development. We reported a 674,152,735 Mbp genome assembly of Poeciliopsis prolifica in 504 contigs with excellent continuity (contig N50 7.7 Mb) and completeness (BUSCO score 97.2%). A total of 27,227 protein-coding genes were annotated from the merged data sets based on bioinformatic prediction and RNA sequencing and homology evidencesupport. Among them, 19,337 have informative SNPs between the two inbred lines, providing sufficient SNP density to infer allele-specific expression genome-wide. Phylogenomic analyses revealed that Poeciliopsis prolifica diverged from the guppy approximately 19 million years ago. Gene family analysis identified the rapid expansion of families with T-cell activation and other immune-related functions in Poeciliopsis prolifica, which may be functionally related to the evolution of the placenta. Our research provides the necessary resources and the genomic toolkit for investigating parental allele-specific gene expression, which will shed light on the evolution of the placenta and genomic imprinting
Dataset for "Genetic and functional diversity help explain pathogenic, weakly pathogenic, and commensal lifestyles in the genus Xanthomonas"
No full textThe genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their co-occurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life-history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically, the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We gathered evidence for gene flow among co-occurring pathogenic and nonpathogenic strains, suggesting the potential of nonpathogenic strains to act as a reservoir of adaptive traits for pathogenic strains and vice versa. We further identified traits enriched in nonpathogens that suggest a strategy of stress tolerance, rather than avoidance, during their association with a broad range of host plants
Epigenetics in Ecology, Evolution, and Conservation
Full text linkEpigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.Publishedye
BAM files associated with Macaca arctoides hybridization analysis
No full textGenital divergence is thought to contribute to reproductive barriers by establishing a “lock-and-key" mechanism for reproductive compatibility. One such example, Macaca arctoides, the bear macaque, has compensatory changes in both male and female genital morphology as compared to close relatives. M. arctoides also has a complex evolutionary history, having extensive introgression between the fascicularis and sinica macaque species groups. Here, phylogenetic relationships were analyzed via whole-genome sequences from five species, including M. arctoides, and two species each from the putative parental species groups. This analysis revealed ~3x more genomic regions supported placement in the sinica species group as compared to the fascicularis species group. Additionally, introgression analysis of the M. arctoides genome revealed it is a mosaic of recent polymorphisms shared with both species groups. To examine the evolution of their unique genital morphology further, the prevalence of candidate genes involved in genital morphology was compared against genome-wide outliers in various population genetic metrics of diversity, divergence, introgression, and selection, while accounting for background variation in recombination rate. This analysis identified 67 outlier genes, including several genes that influence baculum morphology in mice, which were of interest since the bear macaque has the longest primate baculum. The mean of four of the seven population genetic metrics was statistically different in the candidate genes as compared to the rest of the genome, suggesting that genes involved in genital morphology have increased divergence and decreased diversity beyond expectations. These results highlight specific genes that may have played a role in shaping the unique genital morphology in the bear macaque.PublishedYe
Long-Term Decrease in Coloration: A Consequence of Climate Change?
Full text linkClimate change has been shown to affect fitness-related traits in a wide range of taxa; for instance, warming leads to phenological advancements in many plant and animal species. The influence of climate change on social and secondary sexual traits, which are associated with fitness because of their role as quality signals, is, however, unknown. Here, we use more than 5,800 observations collected on two Mediterranean blue tit subspecies (Cyanistes caeruleus caeruleus and Cyanistes caeruleus ogliastrae) to explore whether blue crown and yellow breast patch colorations have changed over the past 15 years. Our data suggest that coloration has become duller and less chromatic in both sexes. In addition, in the Corsican C.c. ogliastrae, but not in the mainland C.c. caeruleus, the decrease is associated with an increase in temperature at molt. Quantitative genetic analyses do not reveal any microevolutionary change in the color traits over the study period, strongly suggesting that the observed change over time was caused by a plastic response to the environmental conditions. Overall, this study suggests that ornamental colorations could become less conspicuous because of warming, revealing climate change effects on sexual and social ornaments and calling for further research on the proximate mechanisms behind these effects.PublishedYe
Fluctuating environments hinder the ability of female lizards to choose suitable nest sites for their embryos
No full textNesting behavior is an important part of reproduction that affects maternal fitness. Females of most oviparous species choose microhabitats for nesting that have positive effects on embryo development. However, choosing suitable nest microhabitats could be challenging in environments that fluctuate unpredictably. In many reptiles, females avoid nesting in dry microhabitats because eggs rapidly desiccate. In nature, however, microhabitats with suitable hydric conditions at the time of oviposition may eventually become lethally dry during incubation. We designed an experiment to test whether female lizards (Anolis sagrei) avoid nesting in locations with unpredictable fluctuations in substrate moisture and choose sites with stable moist conditions. We provided captive lizards three nest conditions to choose among: 1) substrate that predictably alternated between suitable and lethal moisture conditions, 2) substrate that fluctuated unpredictably between suitable and lethal conditions, and 3) substrate with moisture levels that remained constant. For the constant choice, some females could choose moist substrate (which is suitable for embryos), and others could choose dry substrate (which rapidly desiccates eggs). Females always nested in substrates that were moist at the time of oviposition, regardless of the level of predictability. Additionally, while constantly dry substrate was avoided, females did not distinguish between predictable and unpredictable options, both of which resulted in 100% egg mortality. These results suggest that nest site choice is based on immediate environmental cues, rather than the level of predictability of future conditions of nest sites, which in turn can have negative consequences when environments fluctuate between suitable and unsuitable conditions.Submitte
Racial microaggressions: Their effects on mental and physical health
Full text linkIn this webinar session, Jaena Alabi will present a brief history of racial microaggressions research, focusing on the negative mental and physical health outcomes associated with experiencing subtle racism. Strategies for mitigating the negative effects of racial microaggressions, such as incorporating cultural competence into one’s practice, will also be shared
Data for: Using the red-imported fire ant to study invasive species removal and reinvasion
No full textMulti-Event Study on the Connection Between Subauroral Polarization Streams and Deep Energetic Particle Injections in the Inner Magnetosphere
Full text linkEnergetic electron flux enhancements for 100s keV energies are often observed at low L shells (L < 4) in the inner magnetosphere during geomagnetic storms. However, protons with similar energies do not penetrate as deeply as electrons. Electric fields from subauroral polarization streams (SAPS) have been proposed as a mechanism to explain the difference between the 100s keV electron and proton behavior by altering the particles' drift paths and allowing electrons to access lower L shells than protons. Although the primary signature of SAPS is a strong radial electric field, there are corresponding westward/eastward azimuthal electric fields on the eastern/western regions of the SAPS that cause inward/outward radial transport and a differential response between the oppositely drifting electrons and protons. We examine three events where SAPS were observed by the Van Allen Probes near the same time and L shell range as 100s keV electron enhancements deep within the inner magnetosphere. The observations demonstrate that 100s keV electrons were progressively transported radially inward and trapped at low L shells that were consistent with the spatial extent of the SAPS electric fields. Proton flux enhancements were limited to <100 keV energies and were only observed temporarily in the SAPS region, indicating that these particles were on open drift paths. The particle observations are consistent with the differential drift paths for electrons and protons predicted by a simple SAPS electric field model, suggesting that SAPS play an important role in 100s keV particle dynamics at low L shells in the inner magnetosphere.PublishedYe