Livestock Mortality at Beef Farms with Chronic Wolf (Canis lupus) Depredation in the Western Great Lakes Region (WGLR)

Gray wolf (Canis lupus) depredation on beef calves has been studied extensively in recent years. As wolf populations increase throughout the United States there is a corresponding increase in wolf/livestock interactions. Most research concentrates on summaries of reported depredations and surveys of producers affected by depredations. The objective of this study was to present data on the fate of beef calves on 3 farms in Minnesota and Wisconsin over a 2-year period. Predator presence/absence was studied as an indicator of potential depredations. Also, data are presented comparing 2 techniques that may aid researchers and livestock producers with monitoring livestock. Radio telemetry collars and ear tags were applied to beef calves on 3 farms in northern Minnesota and Wisconsin during the spring and summer of 2006 and 2007. During this time, 4 calves were killed by wolves on the study farms. Wolves did not appear to be selecting the youngest calves and most depredations occurred from April through July. Although not statistically significant, wolf sign appeared at slightly higher rates on study farms than on land adjacent to these farms. Predator sign, including coyote (Canis latrans) and black bear (Ursus americanus), appeared more often in the heavily forested areas of the farms. Radio collars and radio ear tags were helpful for monitoring beef calves during this study. Radio collars had much longer transmitting distances than ear tags (2.3 ± 0.8 miles and 0.4 ± 0.2 miles, respectively). Radio ear tags had a potential for causing beef calves\u27 ears to droop or were ripped out, possibly lowering their market value. Currently, cost is prohibitive for the widespread use of radio transmitters for monitoring livestock but as the price of new technologies decreases, transmitters may become an integral part of livestock production on farms with chronic wolf depredation

Livestock mortality at beef farms with chronic wolf ( Canis lupus) depredation in the western Great Lakes region (WGLR)

Gray wolf (Canis lupus) depredation on beef calves has been studied extensively in recent years. As wolf populations increase throughout the United States there is a corresponding increase in wolf/livestock interactions. Most research concentrates on summaries of reported depredations and surveys of producers affected by depredations. The objective of this study was to present data on the fate of beef calves on 3 farms in Minnesota and Wisconsin over a 2-year period. Predator presence/absence was studied as an indicator of potential depredations. Also, data are presented comparing 2 techniques that may aid researchers and livestock producers with monitoring livestock. Radio telemetry collars and ear tags were applied to beef calves on 3 farms in northern Minnesota and Wisconsin during the spring and summer of 2006 and 2007. During this time, 4 calves were killed by wolves on the study farms. Wolves did not appear to be selecting the youngest calves and most depredations occurred from April through July. Although not statistically significant, wolf sign appeared at slightly higher rates on study farms than on land adjacent to these farms. Predator sign, including coyote ( Canis latrans) and black bear (Ursus americanus), appeared more often in the heavily forested areas of the farms. Radio collars and radio ear tags were helpful for monitoring beef calves during this study. Radio collars had much longer transmitting distances than ear tags (2.3 ± 0.8 miles and 0.4 ± 0.2 miles, respectively). Radio ear tags had a potential for causing beef calves' ears to droop or were ripped out, possibly lowering their market value. Currently, cost is prohibitive for the widespread use of radio transmitters for monitoring livestock but as the price of new technologies decreases, transmitters may become an integral part of livestock production on farms with chronic wolf depredation

Sliding window analysis of model fit across <i>Agelaius</i> control region and ND2 regions.

<p>Each point plots parameter values of either an HKY85+G₁₂ (for CR, left), or HKY85+I (for ND2, right) model, for a 250 base pair window centered at that position, for each position sampled (step size = 1). The upper panels show values of the transition/transversion ratio (left axis and black line; some spurious values estimated due to the absence of transversions in given windows omitted), and the parameter of the discrete Γ approximation (CR; 12 categories) or proportion of invariant sites (ND2; right axes and gray lines). The lower panels show the nucleotide proportion parameters π_i.</p

Contrasting Evolutionary Dynamics and Information Content of the Avian Mitochondrial Control Region and ND2 Gene

<div><p>Mitochondrial DNA is an important tool for inference of population history in animals. A variety of mitochondrial loci have been sampled for this purpose, but many studies focus on the non-coding D-loop or control region (CR), which in at least some species appears hypermutable. Unfortunately, analyses of this region are sometimes complicated by segmental duplications, as well as by difficulties in sequencing through repeat expansions, driving many researchers to favor single-copy protein-coding or ribosomal RNA genes. Without systematic comparison, it is unclear if, how much, and what sort of information might be lost by focusing on coding regions, or conversely whether such regions might offer significant advantages over the CR. In this study, we compare the information content, both in terms of genealogy and tests of neutral equilibrium, of the mitochondrial CR and protein-coding ND2 gene of the red-winged blackbird (<em>Agelaius phoeniceus</em>) and its close relative the tricolored blackbird (<em>A. tricolor</em>). Both gene regions violate the standard infinite sites assumption central to moment-based population genetic inference, as well as exhibiting considerable among-site rate heterogeneity, obscuring significant departures from neutral equilibrium. Given the ubiquity of rate heterogeneity in mtDNA, use of more sophisticated tests that account for this should be obligatory. The two regions yield quite similar genealogical reconstructions, as well as indicating similar departures from neutral equilibrium assumptions for <em>A. phoeniceus</em>. However, individual Sanger-read-length fragments (∼600 bases) of the CR have significantly higher information content than comparable fragments of ND2, suggesting that limited sampling of the mitochondrial genome should focus on the CR.</p> </div

Summary of polymorphism data and population parameter estimates in populations of <i>Agelaius phoeniceus</i> and <i>A. tricolor</i>.

<p>L = sequence length, n = number of individuals sampled, <i>k</i> = number of unique haplotypes, <i>h</i> = haplotype diversity (s.d. in parentheses here and subsequently), S = number of segregating sites, η = minimum number of mutations ( = S* of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Misawa1" target="_blank">[42]</a>), I = number of segregating indel mutations, π = nucleotide diversity <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Nei1" target="_blank">[73]</a>, <i>θ_W</i> = Watterson's estimator <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Nei1" target="_blank">[73]</a>, <i>θ_π</i> = Misawa and Tajima's estimator (eqs. 5a and 6a in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Misawa1" target="_blank">[42]</a>), <i>θ_s*</i> = Misawa and Tajima's estimator (eqs. 5c and 6c in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Misawa1" target="_blank">[42]</a>). All calculations of Misawa and Tajima's estimators and test used an α = 0.102 for CR, and α = 0.279 for ND2 (see text, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone-0046403-g002" target="_blank">Figure 2</a>).</p

Tests of neutral equilibrium assumptions in <i>Agelaius phoeniceus</i> and <i>A. tricolor</i>.

<p>Values of Tajima's <i>D</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Tajima1" target="_blank">[36]</a> are accompanied by 95% confidence intervals of the statistic based on the the expected β distribution under the infinite sites model (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone-0046403-t002" target="_blank">table 2</a> in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Tajima1" target="_blank">[36]</a>), and as assessed for data simulated under the best–fit finite-sites model of sequence evolution (FS; see text). Values of Misawa and Tajima's (modified; see Appendices 2 and 3) and of Fu's <i>F_s</i> statistic <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403-Fu1" target="_blank">[37]</a> are also given, along with 95% CIs (or 5^th percentiles for <i>F_S</i>, which is evaluated one-tailed) estimated by simulation as for <i>D</i>. Significance of <i>D</i>, <i>D_s*⁺</i>, and <i>F_s</i> given either the β distribution or coalescent simulations under the infinite sites model (<i>F_s</i> only) is shown by asterisks (*<i>P</i><0.05, **<i>P</i><0.01), and values significant at the α = 0.05 level given finite sites simulation CIs are highlighted in bold.</p

Number of rate categories (k) affects model likelihoods and parameter estimates.

<p>Discrete Γ model negative log-likelihoods for the control region data are shown on the left axis, and estimated α parameters on the right. The line at k = 12 indicates the point at which addition of a class of constant characters (p_iv>0) does not significantly improve the model fit.</p

Maximum likelihood and Bayesian estimates (approximate 95% confidence and credibility intervals in parentheses, parameter estimates for intervals exclusive of 0 are highlighted in bold) of the neutral parameter and population growth for <i>Agelaius phoeniceus</i> and <i>A. tricolor</i>, derived from analyses using LAMARC v2.1.3 [78] and BEAST v1.4.8 [79].

<p>The growth parameter <i>g</i> was either fixed at 0 ( = 0) or allowed to vary (≠0).</p

Rate heterogeneity in <i>Agelaius</i> control region and ND2.

<p>Shown are the inferred number of changes per site (left axis and black line; based on marginal reconstruction of ancestral states on arbitrarily-chosen ML trees) in the alignment of <i>Agelaius</i> CR (above) and ND2 (below), and sliding window analysis (plotted at the center of each window, width = 100 bases, step = 1 base) of site-specific rate estimates (right axis and gray line; empirical Bayes estimates from PAML 4.4, correlation of true and estimated rates was 0.583 for CR and 0.545 for ND2). Asterisks mark five hotspots identified by polymorphism within both <i>A. phoeniceus</i> and <i>A. tricolor</i>, and plus symbols mark “hypervariable” CR sites (defined as sites in the 95^th percentile or higher of site-specific rate estimates for variable sites). Horizontal lines on bars for individual site change reconstructions indicate the number of intraspecific mutations as opposed to fixed differences between species.</p

Trees obtained in maximum likelihood analyses of CR and ND2 data.

<p>Shown are: A) one of ≥270 maximum likelihood trees obtained via heuristic search under the HKY85+G₁₂ model (−lnL = 2907.7, κ = 16.702, π_A = 0.312, π_C = 0.285, π_G = 0.134, α = 0.1019) with a molecular clock, for the set of unique <i>Agelaius</i> CR haplotypes and a single outgroup <i>Molothrus</i> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046403#pone.0046403.s001" target="_blank">Appendix S1</a> for sample identification); and B) the single best tree obtained via heuristic search under the GTR+I model (−lnL = 2337.7, r_AC = 5.122, r_AG = 118.9, r_AT = 3.560, r_CG = 8.226e−4, r_CT = 47.54, π_A = 0.310, π_C = 0.355, π_G = 0.098, <i>p_inv</i> = 0.723) with a molecular clock, for the unique ND2 haplotypes and the same outgroup. Numbers next to branches indicate support as estimated by the non-parametric bootstrap (200 replicates; molecular clock not enforced due to time constraints), and thickened branches indicate estimated Bayesian posterior probabilities ≥0.95.</p