<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xue, Xia</style></author><author><style face="normal" font="default" size="100%">Thompson, Andrew R.</style></author><author><style face="normal" font="default" size="100%">Adams, Byron J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">An Antarctic worm and its soil ecosystem: A review of an emerging research program in ecological genomics</style></title><secondary-title><style face="normal" font="default" size="100%">Applied Soil Ecology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">ecological amplitude</style></keyword><keyword><style  face="normal" font="default" size="100%">ecological succession</style></keyword><keyword><style  face="normal" font="default" size="100%">elemental stoichiometry</style></keyword><keyword><style  face="normal" font="default" size="100%">extreme environments</style></keyword><keyword><style  face="normal" font="default" size="100%">life history evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">model systems</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2024</style></year><pub-dates><date><style  face="normal" font="default" size="100%">01/2024</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://www.sciencedirect.com/science/article/pii/S0929139323003086</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">193</style></volume><pages><style face="normal" font="default" size="100%">105110</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Relationships between the evolution of species and their ecosystems can be difficult to accurately assess due to the high number of confounding biological variables (e.g., biotic interactions among community members and the resulting complex relationships between genetic pathways and organism phenotypes). Thus, progress in ecological genomics by making inferences about fundamental ecological patterns and processes is hampered by high biodiversity and subsequent complex biotic interactions. Study systems that are naturally low in biological and ecological complexity, and strongly structured by abiotic drivers, can serve as models for bridging the gap between controlled mesocosm experiments and natural ecosystems. The terrestrial ecosystems of the Antarctic dry valleys have low biodiversity and constrained ecological complexity, primarily because ecological communities are so strongly shaped by physical, rather than biological, factors. The harsh constraints of the physical environment on organismal evolution and the structure of ecological communities make this an optimal natural system for disentangling the influence of specific environmental parameters on genotype/phenotype and gene by environment interactions. This work reviews the biology, evolution, and ecology of an emerging model organism, the free-living nematode &lt;i&gt;Plectus murrayi&lt;/i&gt;, in a model ecosystem, the McMurdo Dry Valleys (MDVs) of Antarctica. In the MDVs, habitat suitability, including nutrient availability, has been shown to drive organismal (nematode) life history evolution, including growth and reproduction, primarily by way of changes in the expression of developmental genes. Changes in growth rates and reproductive schedules are accomplished primarily through alterations of nuclear rRNA gene copy number. The predicted and observed responses to natural experiments have been replicated in the laboratory, providing a synthesis of field observations and experimental evolution. Studying such natural model systems as this could fill several persistent knowledge gaps in our understanding of how genetic variation, genomic architecture, and gene regulation drive the genotype-phenotype paradigm, and the consequent effects of these drivers on ecosystem structure and functioning.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xue, Xia</style></author><author><style face="normal" font="default" size="100%">Bishwo N. Adhikari</style></author><author><style face="normal" font="default" size="100%">Ball, Becky</style></author><author><style face="normal" font="default" size="100%">John E. Barrett</style></author><author><style face="normal" font="default" size="100%">Miao, Jinxin</style></author><author><style face="normal" font="default" size="100%">Perkes, Ammon</style></author><author><style face="normal" font="default" size="100%">Martin, Mac</style></author><author><style face="normal" font="default" size="100%">Breana L. Simmons</style></author><author><style face="normal" font="default" size="100%">Diana H. Wall</style></author><author><style face="normal" font="default" size="100%">Byron Adams</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Ecological stoichiometry drives the evolution of soil nematode life history traits</style></title><secondary-title><style face="normal" font="default" size="100%">Soil Biology and Biochemistry</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">elemental stoichiometry</style></keyword><keyword><style  face="normal" font="default" size="100%">growth rate hypothesis</style></keyword><keyword><style  face="normal" font="default" size="100%">life history theory</style></keyword><keyword><style  face="normal" font="default" size="100%">molecular evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">nematoda</style></keyword><keyword><style  face="normal" font="default" size="100%">rRNA</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">02/2023</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://www.sciencedirect.com/science/article/pii/S0038071722003480</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">177</style></volume><pages><style face="normal" font="default" size="100%">108891</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Ecological stoichiometry is a useful theoretical framework for understanding the sources and controls on nutrient availability that structure the composition and diversity of biotic communities. One such relationship is that organismal development rate is positively linked to cellular Phosphorus (P). We hypothesized that P availability, relative to other nutrients, e.g., nitrogen and carbon, would drive the evolution of traits associated with organismal growth and development. We examined the effects of P availability both &lt;i&gt;in situ&lt;/i&gt; and &lt;i&gt;in vitro&lt;/i&gt;, on free-living soil nematodes. We found that P-deficient environments produce predictable changes in the ecology and evolution of important life history traits. Our results identify altered rRNA gene copy number and subsequent changes in gene expression and protein synthesis as mechanisms by which P-deficiency influences these traits. These findings have important implications for explaining soil ecological and evolutionary patterns across multiple levels of organization, including the structure and functioning of organisms, populations, communities, and ecosystems.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Robinson, Colin Michael</style></author><author><style face="normal" font="default" size="100%">Hansen, Lee D.</style></author><author><style face="normal" font="default" size="100%">Xue, Xia</style></author><author><style face="normal" font="default" size="100%">Adams, Byron J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Temperature response of metabolic activity of an Antarctic nematode</style></title><secondary-title><style face="normal" font="default" size="100%">Biology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Antarctica</style></keyword><keyword><style  face="normal" font="default" size="100%">carbon cycling</style></keyword><keyword><style  face="normal" font="default" size="100%">climate change</style></keyword><keyword><style  face="normal" font="default" size="100%">nematode</style></keyword><keyword><style  face="normal" font="default" size="100%">respiration rates</style></keyword><keyword><style  face="normal" font="default" size="100%">soil temperature</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2023</style></year><pub-dates><date><style  face="normal" font="default" size="100%">01/2023</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://www.mdpi.com/2079-7737/12/1/109</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">12</style></volume><pages><style face="normal" font="default" size="100%">109</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Because of climate change, the McMurdo Dry Valleys of Antarctica (MCM) have experienced an increase in the frequency and magnitude of summer pulse warming and surface ice and snow melting events. In response to these environmental changes, some nematode species in the MCM have experienced steady population declines over the last three decades, but &lt;i&gt;Plectus murrayi&lt;/i&gt;, a mesophilic nematode species, has responded with a steady increase in range and abundance. To determine how &lt;i&gt;P. murrayi&lt;/i&gt; responds to increasing temperatures, we measured metabolic heat and CO&lt;sub&gt;2&lt;/sub&gt; production rates and calculated O&lt;sub&gt;2&lt;/sub&gt; consumption rates as a function of temperature at 5 &amp;deg;C intervals from 5 to 50 &amp;deg;C. Heat, CO&lt;sub&gt;2&lt;/sub&gt; production, and O&lt;sub&gt;2&lt;/sub&gt; consumption rates increase approximately exponentially up to 40 &amp;deg;C, a temperature never experienced in their polar habitat. Metabolic rates decline rapidly above 40 &amp;deg;C and are irreversibly lost at 50 &amp;deg;C due to thermal stress and mortality. &lt;i&gt;Caenorhabditis elegans&lt;/i&gt;, a much more widespread nematode that is found in more temperate environments reaches peak metabolic heat rate at just 27 &amp;deg;C, above which it experiences high mortality due to thermal stress. At temperatures from 10 to 40 &amp;deg;C, &lt;i&gt;P. murrayi&lt;/i&gt; produces about 6 times more CO&lt;sub&gt;2&lt;/sub&gt; than the O&lt;sub&gt;2&lt;/sub&gt; it consumes, a respiratory quotient indicative of either acetogenesis or de novo lipogenesis. No potential acetogenic microbes were identified in the &lt;i&gt;P. murrayi&lt;/i&gt; microbiome, suggesting that &lt;i&gt;P. murrayi&lt;/i&gt; is producing increased CO&lt;sub&gt;2&lt;/sub&gt; as a byproduct of de novo lipogenesis. This phenomenon, in conjunction with increased summer temperatures in their polar habitat, will likely lead to increased demand for carbon and subsequent increases in CO&lt;sub&gt;2&lt;/sub&gt; production, population abundance, and range expansion. If such changes are not concomitant with increased carbon inputs, we predict the MCM soil ecosystems will experience dramatic declines in functional and taxonomic diversity.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xue, Xia</style></author><author><style face="normal" font="default" size="100%">Adams, Byron J.</style></author><author><style face="normal" font="default" size="100%">Dilman, Adler R.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A draft mitogenome of &lt;i&gt;Plectus murrayi&lt;/i&gt;</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Nematology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Antarctica</style></keyword><keyword><style  face="normal" font="default" size="100%">genome decay</style></keyword><keyword><style  face="normal" font="default" size="100%">genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">mitochondrial genome</style></keyword><keyword><style  face="normal" font="default" size="100%">MitoZ</style></keyword><keyword><style  face="normal" font="default" size="100%">phylogeny</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2022</style></year><pub-dates><date><style  face="normal" font="default" size="100%">02/2022</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://www.sciendo.com/article/10.2478/jofnem-2022-0035https://www.sciendo.com/pdf/10.2478/jofnem-2022-0035</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">54</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;i&gt;Plectus murrayi&lt;/i&gt; is a free-living microbivorous nematode endemic to Antarctic soils. Our draft assembly of its mitogenome was 15,656 bp long, containing 12 protein-coding, eight transfer RNA (tRNA), and two ribosomal RNA (rRNA) genes. Mitophylogenomic analyses extend our understanding of mitochondrial evolution in Nematoda&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xue, Xia</style></author><author><style face="normal" font="default" size="100%">Suvorov, Anton</style></author><author><style face="normal" font="default" size="100%">Fujimoto, Stanley</style></author><author><style face="normal" font="default" size="100%">Dilman, Adler R.</style></author><author><style face="normal" font="default" size="100%">Byron Adams</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome analysis of &lt;I&gt;Plectus murrayi&lt;/I&gt;, a nematode from continental Antarctica</style></title><secondary-title><style face="normal" font="default" size="100%">G3 Genes|Genomes|Genetics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">gene loss</style></keyword><keyword><style  face="normal" font="default" size="100%">genome architecture</style></keyword><keyword><style  face="normal" font="default" size="100%">genome assembly</style></keyword><keyword><style  face="normal" font="default" size="100%">genome decay</style></keyword><keyword><style  face="normal" font="default" size="100%">Plectus murrayi</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2021</style></year><pub-dates><date><style  face="normal" font="default" size="100%">01/2021</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkaa045/6044189</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;em&gt;Plectus murrayi&lt;/em&gt; is one of the most common and locally abundant invertebrates of continental Antarctic ecosystems. Because it is readily cultured on artificial medium in the laboratory and highly tolerant to an extremely harsh environment, &lt;em&gt;Plectus murrayi&lt;/em&gt; is emerging as a model organism for understanding the evolutionary origin and maintenance of adaptive responses to multiple environmental stressors, including freezing and desiccation. The de novo assembled genome of &lt;em&gt;Plectus murrayi&lt;/em&gt; contains 225.741 million base pairs and a total of 14,689 predicted genes. Compared to &lt;em&gt;Caenorhabditis elegans&lt;/em&gt;, the architectural components of &lt;em&gt;Plectus murrayi&lt;/em&gt; are characterized by a lower number of protein-coding genes, fewer transposable elements, but more exons, than closely related taxa from less harsh environments. We compared the transcriptomes of lab-reared &lt;em&gt;Plectus murrayi&lt;/em&gt; with wild-caught &lt;em&gt;Plectus murrayi&lt;/em&gt; and found genes involved in growth and cellular processing were up-regulated in lab-cultured &lt;em&gt;Plectus murrayi&lt;/em&gt;, while a few genes associated with cellular metabolism and freeze tolerance were expressed at relatively lower levels. Preliminary comparative genomic and transcriptomic analyses suggest that the observed constraints on &lt;em&gt;P. murrayi&lt;/em&gt; genome architecture and functional gene expression, including genome decay and intron retention, may be an adaptive response to persisting in a biotically simplified, yet consistently physically harsh environment.&lt;/p&gt;</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>32</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xue, Xia</style></author><author><style face="normal" font="default" size="100%">Byron Adams</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomics and transcriptomics of Antarctic nematodes reveal drivers of life history evolution and genome evolution</style></title><secondary-title><style face="normal" font="default" size="100%">Department of Biology</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Antarctic nematodes</style></keyword><keyword><style  face="normal" font="default" size="100%">Caenorhabditis elegans</style></keyword><keyword><style  face="normal" font="default" size="100%">genome evolution</style></keyword><keyword><style  face="normal" font="default" size="100%">growth rate hypothesis</style></keyword><keyword><style  face="normal" font="default" size="100%">Plectus murrayi</style></keyword><keyword><style  face="normal" font="default" size="100%">Scottnema lindsayae</style></keyword><keyword><style  face="normal" font="default" size="100%">transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://search.proquest.com/docview/2081899003</style></url></web-urls></urls><publisher><style face="normal" font="default" size="100%">Brigham Young University</style></publisher><pub-location><style face="normal" font="default" size="100%">Provo, UT</style></pub-location><volume><style face="normal" font="default" size="100%">Ph.D.</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Elemental stoichiometry defines a critical understanding of the relationship between&amp;nbsp;nutrient availability and usage throughout different levels of the biological community. We&amp;nbsp;found there is a link between available phosphorus (P), cellular phosphorus, and nematode development as postulated by the growth rate hypothesis (GRH). I predicted that in a P-poor environment, cellular RNA concentrations would be lower than they are in P-rich environment, and thus the 18srRNA expression level will have reduced. To most efficiently regulate the&amp;nbsp;uptake of limited P, I predicted that nematodes in P-poor environments would decrease the number of copies of the 18s rRNA gene in their genome. I measured life history traits as well as rRNA gene expression and gene copy number. We found that elemental stoichiometry predicts evolutionary changes consistent with the Growth Rate Hypothesis. We sequenced and assembled a draft genome of &lt;em&gt;P. murrayi&lt;/em&gt;. Although we expected to find genes responsible for stress tolerance, we hypothesized that in response to strong selection pressure associated with living in&amp;nbsp;a simplified ecosystem, over time the genome of &lt;em&gt;P. murrayi&lt;/em&gt; should have undergone significant decay (gene loss) relative to species in ecosystems structured more strongly by biotic interactions. We found significantly fewer genes in &lt;em&gt;P. murrayi&lt;/em&gt;. To compare patterns of gene expression between two highly divergent Antarctic nematode species, we sequenced and assembled the transcriptomes of &lt;em&gt;S. lindsayae&lt;/em&gt; and &lt;em&gt;P. murrayi&lt;/em&gt;. Under laboratory conditions at 4&amp;nbsp; ̊C, &lt;em&gt;S. lindsayae&lt;/em&gt; had significantly lower rates of gene expression but expressed a significantly larger number of genes. We speculate that the differences in gene expression are correlated with life history traits (developmental rates) while the differences in the number of genes expressed can be explained&amp;nbsp;by their different genetic systems (&lt;em&gt;S. lindsayae&lt;/em&gt; is amphimictic, &lt;em&gt;P. murrayi&lt;/em&gt; is parthenogenic) and the soil environments to which they are adapted. Since we previously showed that differences in available P content can influence the evolution of gene expression via gene copy number, and that this ultimately influences growth rate, we wondered how much of this response is driven by genetics versus how strongly these patterns are driven by temperature. To better understand this, we maintained wild type populations of P. murrayi in P-rich and P-poor conditions at 5&amp;nbsp; ̊C, 10&amp;nbsp; ̊C and 15 ̊C in the laboratory for over 40 generations and sequenced the transcriptomes prepared from each treatment group. We found that nutrient levels played an important role in gene expression when the temperature is optimal for P. murrayi culturing and that temperature is more important in gene expression when the available P is limited. This work underscores the utility of using principles of elemental stoichiometry coupled with genomic and transcriptomics research tools to make and test predictions about life history evolution. The results of my work also&amp;nbsp;inform inferences about the ways in which nutrient availability also drives the organization of trophic interactions and ultimately ecosystems.&lt;/p&gt;</style></abstract><work-type><style face="normal" font="default" size="100%">doctoral</style></work-type></record></records></xml>