@article {4583, title = {Genome analysis of Plectus murrayi, a nematode from continental Antarctica}, journal = {G3 Genes|Genomes|Genetics}, year = {2021}, month = {01/2021}, abstract = {

Plectus murrayi 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, Plectus murrayi 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 Plectus murrayi contains 225.741 million base pairs and a total of 14,689 predicted genes. Compared to Caenorhabditis elegans, the architectural components of Plectus murrayi 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 Plectus murrayi with wild-caught Plectus murrayi and found genes involved in growth and cellular processing were up-regulated in lab-cultured Plectus murrayi, 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 P. murrayi 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.

}, keywords = {LTER-MCM, gene loss, genome architecture, genome assembly, genome decay, Plectus murrayi}, doi = {10.1093/g3journal/jkaa045}, url = {https://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkaa045/6044189}, author = {Xue, Xia and Suvorov, Anton and Fujimoto, Stanley and Dilman, Adler R. and Byron Adams} } @article {4488, title = {Genetic diversity of soil invertebrates corroborates timing estimates for past collapses of the West Antarctic Ice Sheet}, journal = {Proceedings of the National Academy of Sciences}, year = {2020}, month = {08/2020}, abstract = {

During austral summer field seasons between 1999 and 2018, we sampled at 91 locations throughout southern Victoria Land and along the Transantarctic Mountains for six species of endemic microarthropods (Collembola), covering a latitudinal range from 76.0\°S to 87.3\°S. We assembled individual mitochondrial cyto-chrome c oxidase subunit 1 (COI) sequences (n = 866) and found high levels of sequence divergence at both small (\<10 km) and large (\>600 km) spatial scales for four of the six Collembola species. We applied molecular clock estimates and assessed genetic divergences relative to the timing of past glacial cycles, including collapses of the West Antarctic Ice Sheet (WAIS). We found that genetically distinct lineages within three species have likely been isolated for at least 5.54 My to 3.52 My, while the other three species diverged more recently (\<2 My). We suggest that Collembola had greater dispersal opportunities under past warmer climates, via flotation along coastal margins. Similarly increased opportunities for dispersal may occur under contemporary climate warming scenarios, which could influence the genetic structure of extant populations. As Collembola are a living record of past landscape evolution within Antarctica, these findings provide biological evidence to support geological and glaciological estimates of historical WAIS dynamics over the last ca. 5 My.

}, keywords = {LTER-MCM, climate change, microarthropods, molecular clock, phylogeography, terrestrial biodiversity}, doi = {10.1073/pnas.2007925117}, url = {https://www.pnas.org/content/early/2020/08/19/2007925117}, author = {Gemma E. Collins and Hogg, Ian D. and Convey, Peter and Sancho, Leopoldo G. and Cowan, Don A. and W. Berry Lyons and Byron Adams and Diana H. Wall and Allan Green, T. G.} } @article {4471, title = {Geochemistry of aeolian material from the McMurdo Dry Valleys, Antarctica: Insights into Southern Hemisphere dust sources}, journal = {Earth and Planetary Science Letters}, volume = {547}, year = {2020}, month = {10/2020}, abstract = {

In the Southern Hemisphere, the major sources of dust and other aeolian materials are from Patagonia, South Africa, Australia, and New Zealand. Dust from Patagonia and New Zealand has been identified in ice cores throughout Antarctica, suggesting that during arid and windy periods, such as glacial periods, dust can be entrained and transported onto the continent. However, little information exists on modern Antarctic dust sources, transport, and its role in the Southern Hemisphere dust cycle. We present the first geochemical characterization of aeolian materials collected at five heights (between 5 cm and 100 cm) above the surface in four valleys within the McMurdo Dry Valleys, the largest ice-free area in Antarctica. Our mineralogy data indicate that these materials are primarily derived from local rocks of the McMurdo Volcanics, Ferrar Dolerite, Beacon Sandstone and Granite Harbor Intrusives, with varying contributions of each rock type dependent on the valley location. While major oxide, trace element and rare earth element data show that low elevation and coastal locations (with respect to the Ross Sea) are dominated by local sources, high elevation and inland locations have accumulated both local materials and dust from other distant Southern Hemisphere sources. This far-traveled material may not be accumulating today, but represents a paleo source that is resuspended from the soils. By geochemically \“fingerprinting\” aeolian materials from the MDV, we can better inform future studies on the transport of materials within Antarctica and between Southern Hemisphere land masses.

}, keywords = {LTER-MCM, aeolian material, Antarctica, major oxides, mineralogy, rare earth elements, trace elements}, doi = {10.1016/j.epsl.2020.116460}, url = {https://www.sciencedirect.com/science/article/pii/S0012821X20304040}, author = {Melisa A. Diaz and Welch, Susan A. and Sheets, J. M. and Kathleen A. Welch and Khan, Alia L. and Byron Adams and Diane M. McKnight and Craig S Cary and W. Berry Lyons} } @article {4420, title = {A global database of soil nematode abundance and functional group composition}, journal = {Scientific Data}, volume = {7}, year = {2020}, month = {03/2020}, abstract = {

As the most abundant animals on earth, nematodes are a dominant component of the soil community. they play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here,\ we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether,\ this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.

}, keywords = {LTER-MCM}, doi = {10.1038/s41597-020-0437-3}, url = {https://www.nature.com/articles/s41597-020-0437-3}, author = {van den Hoogen, Johan and Geisen, Stefan and Diana H. Wall and Wardle, D and Traunspurger, Walter and de Goede, Ron G. M. and Byron Adams and Ahmad, Wasim and Ferris, Howard and Richard D. Bardgett and Bonkowski, Michael and Campos-Herrera, Raquel and Cares, Juvenil E. and Caruso, Tancredi and de Brito Caixeta, Larissa and Chen, Xiaoyun and Costa, Sofia R. and Creamer, Rachel and da Cunha e Castro, Jos{\'e} and Dam, Marie and Djigal, Djibril and Escuer, Miguel and Griffiths, Bryan S. and Guti{\'e}rrez, Carmen and Hohberg, Karin and Kalinkina, Daria and Kardol, Paul and Kergunteuil, Alan and Korthals, Gerard and Krashevska, Valentyna and Kudrin, Alexey A. and Li, Qi and Liang, Wenju and Magilton, Matthew and Marais, Mariette and Mart{\'\i}n, Jos{\'e} Antonio Rodr{\'\i}guez and Matveeva, Elizaveta and Mayad, El Hassan and Mzough, E. and Mulder, Christian and Mullin, Peter and Neilson, Roy and Nguyen, T. A. Duong and Uffe N. Nielsen and Okada, Hiroaki and Rius, Juan Emilio Palomares and Pan, Kaiwen and Peneva, Vlada and Pellissier, Lo{\"\i}c and Carlos Pereira da Silva, Julio and Pitteloud, Camille and Powers, Thomas O. and Powers, Kirsten and Quist, Casper W. and Rasmann, Sergio and Moreno, Sara S{\'a}nchez and Scheu, Stefan and Set{\"a}l{\"a}, Heikki and Sushchuk, Anna and Tiunov, Alexei V. and Trap, Jean and Vesterg{\r a}rd, Mette and Villenave, Cecile and Waeyenberge, Lieven and Wilschut, Rutger and Wright, Daniel G. and Keith, Aidan M. and Yang, Jiue-in and Schmidt, Olaf and Bouharroud, R. and Ferji, Z. and van der Putten, Wim H. and Routh, Devin and Crowther, Thomas Ward} } @phdthesis {4363, title = {Genomics and transcriptomics of Antarctic nematodes reveal drivers of life history evolution and genome evolution}, volume = {Ph.D.}, year = {2018}, school = {Brigham Young University}, type = {doctoral}, address = {Provo, UT}, abstract = {

Elemental stoichiometry defines a critical understanding of the relationship between\ nutrient availability and usage throughout different levels of the biological community. We\ 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\ 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 P. murrayi. Although we expected to find genes responsible for stress tolerance, we hypothesized that in response to strong selection pressure associated with living in\ a simplified ecosystem, over time the genome of P. murrayi should have undergone significant decay (gene loss) relative to species in ecosystems structured more strongly by biotic interactions. We found significantly fewer genes in P. murrayi. To compare patterns of gene expression between two highly divergent Antarctic nematode species, we sequenced and assembled the transcriptomes of S. lindsayae and P. murrayi. Under laboratory conditions at 4\  ̊C, S. lindsayae 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\ by their different genetic systems (S. lindsayae is amphimictic, P. murrayi 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\  ̊C, 10\  ̊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\ inform inferences about the ways in which nutrient availability also drives the organization of trophic interactions and ultimately ecosystems.

}, keywords = {LTER-MCM, Antarctic nematodes, Caenorhabditis elegans, genome evolution, growth rate hypothesis, Plectus murrayi, Scottnema lindsayae, transcriptome}, url = {https://search.proquest.com/docview/2081899003}, author = {Xue, Xia and Byron Adams} } @article {4014, title = {Genetic diversity among populations of Antarctic springtails (Collembola) within the Mackay Glacier ecotone 1}, journal = {Genome}, volume = {59}, year = {2016}, month = {Jan-09-2016}, pages = {762 - 770}, keywords = {LTER-MCM}, issn = {0831-2796}, doi = {10.1139/gen-2015-0194}, url = {http://www.nrcresearchpress.com/doi/10.1139/gen-2015-0194}, author = {Clare R. Beet and Hogg, Ian D. and Gemma E. Collins and Cowan, Don A. and Diana H. Wall and Byron Adams and John-James Wilson} } @phdthesis {4442, title = {Genomic analysis of nematode-environment interaction}, volume = {Ph.D.}, year = {2010}, month = {08/2010}, school = {Brigham Young University}, type = {doctoral}, address = {Provo, UT}, abstract = {

The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression during anhydrobiosis of the Antarctic nematode Plectus murrayi was undertaken. An EST library representative of the desiccation induced transcripts was established and the transcripts differentially expressed during desiccation stress were identified. The expressed genome of P. murrayi showed that desiccation survival in nematodes involves differential expression of a suite of genes from diverse functional areas, and constitutive expression of a number of stress related genes. My study also revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress related genes, improves desiccation and freezing survival of nematodes. Deterioration of traits essential for biological control has been recognized in diverse biological control agents including insect pathogenic nematodes. I studied the genetic mechanisms behind such deterioration using expression profiling. My results showed that trait deterioration of insect pathogenic nematode induces substantial overall changes in the nematode transcriptome and exhibits a general pattern of metabolic shift causing massive changes in metabolic and other processes. Finally, through field observations and molecular laboratory experiments the validity of the growth rate hypothesis in natural populations of Antarctic nematodes was tested. My results indicated that elemental stoichiometry influences evolutionary adaptations in gene expression and genome evolution. My study, in addition to providing immediate insight into the mechanisms by which multicellular animals respond to their environment, is transformative in its potential to inform other fundamental ecological and evolutionary questions, such as the evolution of life-history patterns and the relationship between community structure and ecological function in ecosystems.

}, keywords = {LTER-MCM, anhydrobiosis, Antarctic nematode, comparative transcriptomics, complementary DNA library, desiccation, functional analysis, Heterorhabditis bacteriophora, McMurdo Dry Valleys, microarray analysis, Plectus murrayi, quantative real-time polymerase chain reaction, Scottnema lindsayae, stoichiometry, stress survival, subtractive hybridization, trait deterioration, transcriptional profiling}, url = {https://scholarsarchive.byu.edu/etd/2578}, author = {Bishwo N. Adhikari and Byron Adams} }