A pseudomolecule assembly of the Rocky Mountain elk genome

Rocky Mountain elk (Cervus canadensis) populations have significant economic implications to the cattle industry, as they are a major reservoir for Brucella abortus in the Greater Yellowstone area. Vaccination attempts against intracellular bacterial diseases in elk populations have not been successful due to a negligible adaptive cellular immune response. A lack of genomic resources has impeded attempts to better understand why vaccination does not induce protective immunity. To overcome this limitation, PacBio, Illumina, and Hi-C sequencing with a total of 686-fold coverage was used to assemble the elk genome into 35 pseudomolecules. A robust gene annotation was generated resulting in 18,013 gene models and 33,422 mRNAs. The accuracy of the assembly was assessed using synteny to the red deer and cattle genomes identifying several chromosomal rearrangements, fusions and fissions. Because this genome assembly and annotation provide a foundation for genome-enabled exploration of Cervus species, we demonstrate its utility by exploring the conservation of immune system-related genes. We conclude by comparing cattle immune system-related genes to the elk genome, revealing eight putative gene losses in elk.

Forecasting eco-evolutionary dynamics in the Northern Blue butterfly (2019 field season)

Natural selection can drive rapid evolutionary change, particularly in human-altered habitats. Rapid adaptation to global change requires standing genetic variation for ecologically important traits, but at present little is known about how much relevant genetic variation most populations possess. With this in mind, we began a long term study of genome-wide molecular evolution in a series of natural butterfly populations in the Greater Yellowstone Area in 2012 to quantify the contribution of environment-dependent natural selection to evolution in these butterfly populations, and determine whether selection varies enough across space and time to maintain variation that could facilitate adaptation to global change. In 2019, we visited 11 focal populations to collect samples for DNA and plant chemistry, estimate population sizes (mark-release-recapture methods), and survey arthropod communities at the sites. Our analyses are ongoing, and this is a preliminary report, but thus far we have found that census population sizes are much higher than contemporary effective population sizes (though these metrics are highly correlated), and that both are independent of genetic diversity levels. These results are consistent with the hypothesis that selection plays a central role in eco-evolutionary dynamics in this system. Featured photo from figure 1 in report.

Forecasting eco-evolutionary dynamics in the Northern Blue butterfly (Lycaeides idas)

Natural selection can drive rapid evolutionary change, particularly in human-altered habitats. Rapid adaptation to global change requires standing genetic variation for ecologically important traits, but at present little is known about how much relevant genetic variation most populations possess. With this in mind, we began a long term study of genome-wide molecular evolution in a series of natural butterfly populations in the Greater Yellowstone Area (GYA) in 2012 to quantify the contribution of environment-dependent natural selection to evolution in these butterfly populations, and determine whether selection varies enough across space and time to maintain variation that could facilitate adaptation to global change. In 2018, we visited 11 focal populations to collect samples for DNA, estimate population sizes (using distance sampling and mark-release-recapture methods), and survey arthropod communities at the sites. Our analyses are ongoing, and this is a preliminary report, but thus far we have found that census population sizes are much higher than contemporary effective population sizes (though these metrics are highly correlated), and that both are independent of genetic diversity levels. These results are consistent with the hypothesis that selection plays a central role in eco-evolutionary dynamics in this system. Featured photo from Figure 1 in report.

Source regions contributing to excess reactive nitrogen deposition in the Greater Yellowstone Area (GYA) of the United States

Research has shown that excess reactive nitrogen (Nr) deposition in the Greater Yellowstone Area (GYA) of the United States has passed critical load (CL) thresholds and is adversely affecting sensitive ecosystems in this area. To better understand the sources causing excess Nr deposition, the Comprehensive Air Quality Model with Extensions (CAMx), using Western Air Quality Study (WAQS) emission and meteorology inputs, was used to simulate Nr deposition in the GYA. CAMx's Particulate Source Apportionment Technology (PSAT) was employed to estimate contributions from agriculture (AG), oil and gas (OG), fire (Fire), and other (Other) source sectors from 27 regions, including the model boundary conditions (BCs) to the simulated Nr for 2011. The BCs were outside the conterminous United States and thought to represent international anthropogenic and natural contributions. Emissions from the AG and Other source sectors are predominantly from reduced N and oxidized N compounds, respectively. The model evaluation revealed a systematic underestimation in ammonia (NH3) concentrations by 65 % and overestimation in nitric acid concentrations by 108 %. The measured inorganic N wet deposition at National Trends Network sites in the GYA was overestimated by 31 %–49 %, due at least partially to an overestimation of precipitation. These uncertainties appear to result in an overestimation of distant source regions including California and BCs and an underestimation of closer agricultural source regions including the Snake River valley. Due to these large uncertainties, the relative contributions from the modeled sources and their general patterns are the most reliable results. Source apportionment results showed that the AG sector was the single largest contributor to the GYA total Nr deposition, contributing 34 % on an annual basis. A total of 74 % of the AG contributions originated from the Idaho Snake River valley, with Wyoming, California, and northern Utah contributing another 7 %, 5 %, and 4 %, respectively. Contributions from the OG sector were small at about 1 % over the GYA, except in the southern Wind River Mountain Range during winter where they accounted for more than 10 %, with 46 % of these contributions coming from OG activities in Wyoming. Wild and prescribed fires contributed 18 % of the total Nr deposition, with fires within the GYA having the highest impact. The Other source category was the largest winter contributor (44 %) with high contributions from California, Wyoming, and northern Utah.

Source regions contributing to excess reactive nitrogen deposition in the Greater Yellowstone Area (GYA) of the United States

Research has shown that excess reactive nitrogen (Nr) deposition in the Greater Yellowstone Area (GYA) of the United States has passed critical load thresholds and is adversely affecting sensitive ecosystems in this area. To better understand the sources causing excess Nr deposition, the Comprehensive Air Quality Model with extensions (CAMx), using Western Air Quality Study (WAQS) emission and meteorology inputs, was used to simulate Nr deposition in the GYA. CAMx's Particulate Source Apportionment Technology (PSAT) was employed to estimate contributions from agriculture (AG), oil and gas (OG), fire (Fire), and other (Other) source sectors from 27 regions, including the model boundary conditions (BC) representative of international contributions, to the simulated Nr for 2011. Emissions from the AG and Other source sectors are predominantly from reduced N and oxidized N compounds, respectively. The model evaluation revealed a systematic underestimation in ammonia (NH3) concentrations by 65 % and overestimation in nitric acid concentrations by 108 %. The measured inorganic N wet deposition at National Trend Network sites in the GYA was overestimated by 31–49 %, due at least partially to an overestimation of precipitation. Source apportionment results showed that the AG sector was the single largest contributor to the GYA total Nr deposition, contributing 34 % on an annual basis. Seventy-four percent of the AG contributions originated from the Idaho Snake River valley, with Wyoming, California, and northern Utah contributing another 7 %, 5 %, 20 and 4 % respectively. Contributions from the OG sector were small at about 1 % over the GYA, except in the southern Wind River Mountain Range during winter where they accounted for more than 10 %, with 46 % of these contributions coming from OG activities in Wyoming. Wild and prescribed fires contributed 18 % of the total Nr deposition, with fires within the GYA having the highest impact. The five largest source area contributions to the annual total Nr deposition in the GYA were 1) the Snake River valley (3 8 % with AG 68 %, OG 2 %, Fire 15 %, and Other 16 %); 2) BC (21 %); 3) Wyoming (12 % with AG 19 %, OG 5 %, Fire 38 %, and Other 39 %); 4) California (7 % with AG 26 %, OG 1 %, Fire 14 %, and Other 59 %); and 5) northern Utah (6 % with AG 25 %, OG 2 %, Fire 10 %, and 25 Other 63 %). These results suggest that Nr deposition over the GYA, especially in the western region, was above the critical loads for sensitive ecosystems, and 22 AG from the Snake River valley was the largest contributor. Distant source regions were also important, with large contributions from the BC, i.e., international source regions.

Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

Long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, with spatial and temporal variation in the strength of selection a critical driver of genetic variation in natural populations. In 2012, we began a long term study of genome-wide molecular evolution in populations of the butterfly Lycaeides ideas in the Greater Yellowstone Area (GYA). We aimed to quantify the role of environment-dependent selection on evolution in these populations. Building on previous work, in 2017 we collected new samples, incorporated distance sampling, and surveyed the insect community at each site. We also defined the habitat boundary at anew, eleventh site. Our preliminary analyses suggest that both genetic drift and selection are important drivers in this system. Featured photo from Figure 1 in report.