Mitochondrial 16s ribosomal gene fragment sequences from killer whale feces

There are 15 fasta files containing DNA sequences from a ~330bp fragment of the mitochondrial 16s ribosomal RNA gene. These sequences were amplified from 175 killer whale feces collected from the wild. The samples are pooled into 13 experimental groups; the numbers in the file names correspond to the sample pools described in Table S1 of the associated publication which contains sampling information (time, location, whale ID if known). Samples 23 and 24 are controls, as described in the publication. Methodological details including primers and sequencing methods are described in the associated publication

Characterizing a Foraging Hotspot for Short-Finned Pilot Whales and Blainville’s Beaked Whales Located off the West Side of Hawai‘i Island by Using Tagging and Oceanographic Data

<div><p>Satellite tagging data for short-finned pilot whales (<i>Globicephala macrorhynchus</i>) and Blainville’s beaked whales (<i>Mesoplodon densirostris</i>) were used to identify core insular foraging regions off the Kona (west) Coast of Hawai‘i Island. Ship-based active acoustic surveys and oceanographic model output were used in generalized additive models (GAMs) and mixed models to characterize the oceanography of these regions and to examine relationships between whale density and the environment. The regions of highest density for pilot whales and Blainville’s beaked whales were located between the 1000 and 2500 m isobaths and the 250 and 2000 m isobaths, respectively. Both species were associated with slope waters, but given the topography of the area, the horizontal distribution of beaked whales was narrower and located in shallower waters than that of pilot whales. The key oceanographic parameters characterizing the foraging regions were bathymetry, temperature at depth, and a high density of midwater micronekton scattering at 70 kHz in 400–650 m depths that likely represent the island-associated deep mesopelagic boundary community and serve as prey for the prey of the whales. Thus, our results suggest that off the Kona Coast, and potentially around other main Hawaiian Islands, the deep mesopelagic boundary community is key to a food web that supports insular cetacean populations.</p></div

Micronekton distribution.

<p>Observed density of micronekton along 2011, 2013, 2014 cruise transects (a–c, respectively), all 3 cruises combined with the “hotspot” and “off-shore” sites circled (d) and corresponding predicted density of micronekton over the study area from the GAM (lon,lat) (e). Values shown here are standardized NASC values for 70 kHz deep night-time. The lettered black dots on Fig 4B represent the 2013 trawling stations.</p

Beaked whale GAMM.

<p>Kernel density estimates for Blainville’s beaked whale density (a), predicted Blainville’s beaked whale density from GAMM (b), smoother from GAMM for bathymetry (c), temperature at 300 m (d), micronekton density in the shallow layer observed on the 70 kHz (e). The two scales are not the same to better reflect where the areas of relative highest densities are, according to the density estimates and the model predictions. Dashed lines represent the confidence intervals around the smoothers.</p

Depth profiles of NASC.

<p>Depth profiles of NASC from the 2011 cruise for the 38 kHz (blue lines) and 70 kHz (black lines) transducers at one inshore location (a-b) and one off-shore location (c-d) during the night-time (left) and the daytime (right). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142628#pone.0142628.g004" target="_blank">Fig 4D</a> for inshore and offshore locations.</p

Summary of all covariates considered in the whale GAMMs: bathymetry, NASC values for 8 components of the micronekton from cruise data, currents absolute and vertical velocities, temperature and salinity at 11 depth levels from a general circulation model.

<p>Summary of all covariates considered in the whale GAMMs: bathymetry, NASC values for 8 components of the micronekton from cruise data, currents absolute and vertical velocities, temperature and salinity at 11 depth levels from a general circulation model.</p

Diel migration.

<p>Bathymetry smoothers from GAMMs for short-finned pilot whales (a), and Blainville’s beaked whales (b), and from GAM for 70 kHz NASC (c), 38 kHz NASC (d). Black and blue lines represent daytime and night-time distributions, respectively. Dashed lines represent the confidence intervals around the smoothers.</p

Deviance explained by the biomass of each micronekton component in a single-variable GAMM for Blainville’s beaked whales and short-finned pilot whales.

<p>Deviance explained by the biomass of each micronekton component in a single-variable GAMM for Blainville’s beaked whales and short-finned pilot whales.</p

Variables in the GAMM for Blainville’s beaked whales and amount of deviance explained by each.

<p>Variables in the GAMM for Blainville’s beaked whales and amount of deviance explained by each.</p

Whale tracks.

<p>Maps of filtered and resampled tracks for short-finned pilot whales (a, n = 46) and Blainville’s beaked whales (b, n = 12). Satellite tag deployment locations are represented with green triangles.</p