Modeling Freshwater Mussel Distribution in Relation to Biotic and Abiotic Habitat Variables in the Middle Fork John Day River, Oregon

The habitat requirements of western freshwater mussels, Anodonta, Gonidea, and Margaritifera, remain unclear despite their imperiled status. Freshwater mussels provide a series of ecosystem services including habitat enhancement, substratum stabilization, nutrient cycling, and water clarification, which makes their loss from aquatic ecosystems particularly detrimental. To improve the efficacy of restoration actions targeting these organisms, I used random forest modeling to investigate the biotic and abiotic factors influencing mussel density and distribution throughout a 55-kilometer (km) segment of the Middle Fork John Day River (MFJDR), in northeastern Oregon. Data was collected to characterize the occurrence of mussels with respect to the hierarchical, hydrogeomorphic structure of habitat within reaches of varying valley confinement and channel units nested within these reaches. Data regarding functional habitat features were also included to ensure that models included the wide range of characteristics that mussels need from their environment. By collecting data at both the reach and channel unit scale, I was able to investigate how mussel densities and distributions vary with spatial scale and other biophysical parameters. Throughout the study area, Margaritifera density exhibited a unimodal distribution with respect to river km, while Anodonta and Gonidea density showed a negative relationship with river km and exhibited higher densities downstream. The large scale, longitudinal trends of Margaritifera were related to hydrogeomorphic characteristics at the reach scale, while less than half of the longitudinal variation in Anodonta and Gonidea were explained by hydrogeomorphic and water quality parameters. At the channel unit scale, all mussel genera responded to the patchy variation in physical habitat characteristics, particularly habitat factors that indicated more stable parts of the channel. Overall, physical habitat characteristics such as woody debris, emergent aquatic vegetation, coarse substratum, and channel morphology were more important than hydraulic, biotic, and chemical variables. These results suggest that at both the reach and channel unit scales, mussel density and distribution are influenced by high flow refugia and the hierarchical structuring of hydrogeomorphic habitat characteristics. These results will assist mussel restoration efforts by providing specific guidance about the types of physical habitat conditions that are suitable for mussels

Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog

The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity (“load”) and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection

Short-Term Space-Use Patterns of Translocated Mojave Desert Tortoise in Southern California.

Increasingly, renewable energy comprises a larger share of global energy production. Across the western United States, public lands are being developed to support renewable energy production. Where there are conflicts with threatened or endangered species, translocation can be used in an attempt to mitigate negative effects. For the threatened Mojave desert tortoise (Gopherus agassizii), we sought to compare habitat- and space-use patterns between short-distance translocated, resident, and control groups. We tested for differences in home range size based on utilization distributions and used linear mixed-effects models to compare space-use intensity, while controlling for demographic and environmental variables. In addition, we examined mean movement distances as well as home range overlap between years and for male and female tortoises in each study group. During the first active season post-translocation, home range size was greater and space-use intensity was lower for translocated tortoises than resident and control groups. These patterns were not present in the second season. In both years, there was no difference in home range size or space-use intensity between control and resident groups. Translocation typically resulted in one active season of questing followed by a second active season characterized by space-use patterns that were indistinguishable from control tortoises. Across both years, the number of times a tortoise was found in a burrow was positively related to greater space-use intensity. Minimizing the time required for translocated tortoises to exhibit patterns similar to non-translocated individuals may have strong implications for conservation by reducing exposure to adverse environmental conditions and predation. With ongoing development, our results can be used to guide future efforts aimed at understanding how translocation strategies influence patterns of animal space use

Model-averaged parameter estimates (β¯~) unconditional standard errors (SE), 95% confidence intervals (CI), and cumulative Akaike’s Information Criterion weights (w₊(<i>j</i>)) for all variables used to model space-use intensity in the combined 2012 and 2013 active seasons.

<p>MCLavg = average midline carapace length in each year. In our design matrix, the categorical variables were specified such that control west, female, and 2012 were the baseline contrasts used for comparison in the study group, sex, and year categories, respectively. Note the negative effect for translocated and positive effect for year × translocated, suggesting that space-use intensity increased for translocated tortoises in 2013 relative to 2012.</p><p>Model-averaged parameter estimates (<math><mrow><mrow><mi>β</mi><mo stretchy="true">¯</mo></mrow><mo>~</mo></mrow></math>) unconditional standard errors (SE), 95% confidence intervals (CI), and cumulative Akaike’s Information Criterion weights (w₊(<i>j</i>)) for all variables used to model space-use intensity in the combined 2012 and 2013 active seasons.</p

Summary of multiple comparisons <i>Z-</i>tests of pairwise differences (Estimate) in mean log-UD (i.e., log-hectares encompassed by the 95% kernel density estimate) among the four tortoise study groups, including standard errors (SE), test statistics (<i>z</i>-value), and adjusted <i>p</i>-values for the 2012 and 2013 active seasons.

<p>CW = control west; CE = control east; RE = resident; TR = translocated. Significant differences were detected between the translocated group and each of other groups in the 2012 active season; no other statistically significant differences were detected.</p><p>Summary of multiple comparisons <i>Z-</i>tests of pairwise differences (Estimate) in mean log-UD (i.e., log-hectares encompassed by the 95% kernel density estimate) among the four tortoise study groups, including standard errors (SE), test statistics (<i>z</i>-value), and adjusted <i>p</i>-values for the 2012 and 2013 active seasons.</p

Estimates of mean percentage overlap of 95% utilization distributions between resident and translocated male and female tortoises monitored during the 2012 and 2013 active seasons combined (approximately April through October).

<p>TT = overlap between tortoises in the translocated study group, RR = overlap between tortoises in the resident study group, and TR = overlap between tortoises in the translocated study group with those in the resident group. Grey bars represent overlap of males with other males and white bars show the percentage of overlap between females. Note that males in all comparisons had greater overlap than did females and those tortoises in the translocated study group had greater overlap for both sexes than in the other comparisons.</p

Number and composition of individual tortoises in each study group during the 2012 and 2013 active seasons, partitioned by average midline carapace length (MCL, in millimeters), MCL standard error (SE_MCL), average utilization distribution (UD, in hectares) and UD standard error (SE_UD).

<p>¹The UD is defined as the area encompassed by the 95% kernel density estimate for each tortoise.</p><p>Number and composition of individual tortoises in each study group during the 2012 and 2013 active seasons, partitioned by average midline carapace length (MCL, in millimeters), MCL standard error (SE_MCL), average utilization distribution (UD, in hectares) and UD standard error (SE_UD).</p

Estimates of mean percentage overlap of 95% utilization distributions between resident and translocated tortoises monitored during the 2012 (grey bars) and 2013 (white bars) active seasons (approximately April through October).

<p>TT = overlap between tortoises in the translocated study group, RR = overlap between tortoises in the resident study group, and TR = overlap between tortoises in the translocated study group with those in the resident group. Note that overlap between translocated study group individuals was more than twice as great in 2012 compared to 2013.</p

Summary of multiple comparisons <i>Z-</i>tests of pairwise differences (Estimate) in mean log-UD (log-hectares encompassed by the 95% kernel density estimate) among the sexes, including standard errors (SE), test statistics (<i>z</i>-value), and adjusted <i>p</i>-values for the 2012 and 2013 active seasons.

<p>F = Female; M = Male; U = Unknown.</p><p>Summary of multiple comparisons <i>Z-</i>tests of pairwise differences (Estimate) in mean log-UD (log-hectares encompassed by the 95% kernel density estimate) among the sexes, including standard errors (SE), test statistics (<i>z</i>-value), and adjusted <i>p</i>-values for the 2012 and 2013 active seasons.</p

Number and composition of individual tortoises by sex during the 2012 and 2013 active seasons, partitioned by average midline carapace length (MCL, in millimeters), MCL standard error (SE_MCL), average utilization distribution area (UD, in hectares) and UD standard error (SE_UD).

<p>¹Tortoises classified as sex = Unknown were overwhelmingly sub-adults too small to be identified as male or female.</p><p>²The UD is defined as the area encompassed by the 95% kernel density estimate for each tortoise.</p><p>Number and composition of individual tortoises by sex during the 2012 and 2013 active seasons, partitioned by average midline carapace length (MCL, in millimeters), MCL standard error (SE_MCL), average utilization distribution area (UD, in hectares) and UD standard error (SE_UD).</p