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1. Population Genomics of Daphnia pulex

   https://doi.org/10.1534/genetics.116.190611  

   Lynch, Michael; Gutenkunst, Ryan; Ackerman, Matthew; Spitze, Ken; Ye, Zhiqiang; Maruki, Takahiro; Jia, Zhiyuan (May 2017, Genetics)

   null (Ed.)

   Abstract Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster. These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short (<100 bp) distances in D. melanogaster and at long distances in D. pulex. The study population adheres closely to the expectations under Hardy–Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies >0.05 appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an ∼2× higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations. 

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2. A GALEX view of the DA white dwarf population

   https://doi.org/10.1093/mnras/stad1699  

   Wall, Renae E; Kilic, Mukremin; Bergeron, P; Leiphart, Nathan D (June 2023, Monthly Notices of the Royal Astronomical Society)

   ABSTRACT We present a detailed model atmosphere analysis of 14001 DA white dwarfs from the Montreal White Dwarf Database with ultraviolet photometry from the GALEX mission. We use the 100 pc sample, where the extinction is negligible, to demonstrate that there are no major systematic differences between the best-fitting parameters derived from optical only data and the optical + UV photometry. GALEX FUV and NUV data improve the statistical errors in the model fits, especially for the hotter white dwarfs with spectral energy distributions that peak in the UV. Fitting the UV to optical spectral energy distributions also reveals UV-excess or UV-deficit objects. We use two different methods to identify outliers in our model fits. Known outliers include objects with unusual atmospheric compositions, strongly magnetic white dwarfs, and binary white dwarfs, including double degenerates and white dwarf + main-sequence systems. We present a list of 89 newly identified outliers based on GALEX UV data; follow-up observations of these objects will be required to constrain their nature. Several current and upcoming large-scale spectroscopic surveys are targeting >105 white dwarfs. In addition, the ULTRASAT mission is planning an all-sky survey in the NUV band. A combination of the UV data from GALEX and ULTRASAT and optical data on these large samples of spectroscopically confirmed DA white dwarfs will provide an excellent opportunity to identify unusual white dwarfs in the solar neighbourhood. 

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3. Environmental and population influences on mummichog ( Fundulus heteroclitus ) gut microbiomes

   https://doi.org/10.1128/spectrum.00947-24  

   Ma, Lei; Hahn, Mark E; Karchner, Sibel I; Nacci, Diane; Clark, Bryan W; Apprill, Amy; Zhang, Zhen (March 2025, Microbiology Spectrum)

   Iwanowicz, Luke R (Ed.)

   ABSTRACT The mummichog,Fundulus heteroclitus, an abundant estuarine fish broadly distributed along the eastern coast of North America, has repeatedly evolved tolerance to otherwise lethal levels of aromatic hydrocarbon exposure. This tolerance is linked to reduced activation of the aryl hydrocarbon receptor (AHR) signaling pathway. In other animals, the AHR has been shown to influence the gastrointestinal-associated microbial community, particularly when activated by the model toxic pollutant 3,3′,4,4′,5-pentachlorobiphenyl (PCB-126) and other dioxin-like compounds. To understand host population and PCB-126 exposure effects on mummichog gut microbiota, we sampled two populations of wild fish, one from a PCB-contaminated environment (New Bedford Harbor, MA, USA) and the other from a much less polluted location (Scorton Creek, MA, USA), as well as laboratory-reared F2 generation fish originating from each of these populations. We examined the microbes associated with the gut of these fish using amplicon sequencing of bacterial and archaeal small subunit ribosomal RNA genes. Fish living in the PCB-polluted site had high microbial alpha and beta diversity compared to fish from the low PCB site. These differences between wild fish were not present in laboratory-reared F2 fish that originated from the same populations. Microbial compositional differences existed between wild and lab-reared fish, with the wild fish dominated by Vibrionaceae and the lab-reared fish by Enterococceae. These results suggest that mummichog habitat and/or environmental conditions have a stronger influence on the mummichog gut microbiome compared to population or hereditary-based influences. Mummichog are important eco-evolutionary model organisms; this work reveals their importance for exploring host-environmental-microbiome dynamics. IMPORTANCEThe mummichog fish, a common resident of North America's east coast estuaries, has evolved the ability to survive in waters contaminated with toxic chemicals that would typically be deadly. Our study investigates how living in and adapting to these toxic environments may affect their gut microbiomes. We compared mummichogs from a polluted area in Massachusetts with those from a non-polluted site and found significant differences in their gut microbes. Interestingly, when we raised the next generation of these fish in a lab, these differences disappeared, suggesting that the environment plays a more crucial role in shaping the gut microbiome than genetics. Understanding these changes helps shed light on how animals and their associated microbiomes adapt to pollution, which can inform conservation efforts and our broader understanding of environmental impacts on host-microbe dynamics. 

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4. Automated high-throughput organic crystal structure prediction via population-based sampling

   https://doi.org/10.1039/D4DD00264D  

   Zhu, Qiang; Hattori, Shinnosuke (January 2025, Digital Discovery)

   With advancements in computational molecular modeling and powerful structure search methods, it is now possible to systematically screen crystal structures for small organic molecules. 

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5. Defining the Unseen: Population-Specific Markers for Astyanax mexicanus Blind Cavefish

   https://doi.org/10.1089/zeb.2023.0105  

   Manning, Aubrey E; Grunwald, Hannah; Moran, Rachel; Rodriguez-Morales, Roberto; Powers, Amanda K; McGaugh, Suzanne; Kowalko, Johanna E (June 2024, Zebrafish)

   Astyanax mexicanus is an emerging model system used to study development, evolution, and behavior of multiple cavefish populations that have repeatedly evolved from conspecific surface fish. Although surface and cavefish live and breed in the laboratory, there are no rapid methods for distinguishing between different cavefish populations. We present 2 methods for genotyping fish for a total of 16 population-specific markers using methods that are easy and inexpensive to implement in a basic molecular biology laboratory. This resource will help researchers maintain independent stocks within the laboratory and distinguish between fish from different populations. 

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