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Figure 4 in Revision of northeast Pacific Paleogene cypraeoidean gastropods, including recognition of three new species: implications for paleobiogeographic distribution and faunal turnover
Figure 4 (previous page). A–C. Nucleolaria cowlitzensis Groves, 1994, Cowlitz Formation (middle Eocene, upper "Tejon Stage"), Vader area, south-central Lewis County, Washington. Basal (A), dorsal (B), and left (columellar) side (C) views, 1.9x, length 27.2 mm, width 17.3 mm, height 11.3 mm, of holotype UCMP 39837, UCMP Locality D-8040. D–H. Propustularia kemperae (Nelson, 1925), Santa Susana Formation, (Paleocene, Selandian Stage), north side Simi Hills, Ventura County, southern California. Basal (D), dorsal (E), and right (labral) side (F), and views, 2.2x, length 21 mm, width 17.3, height 12 mm, of holotype CASG 391.01 [ex CASG 987], Locality CASG 391. Dorsal (G) view, 2.6x, length 18.2 mm, width 14.9, height 11.2 mm, of hypotype LACMIP 22307.6, LACMIP Type 14918 (LACMIP Locality 22307). Basal (H) view, 2.2x, length 21 mm, width 17.3, height 12 mm, of paratype UCMP 30541, UCMP Locality 3764. I–N. Subepona goedertorum (Groves and Squires, 1995), Crescent Formation (Eocene, "Capay Stage"), Black Hills, Thurston County, Washington. Basal (I), dorsal (J), left (columellar) lateral (K), and right (labral) (L) views, 2.8x, length 19.4 mm, width 12.3, height 10.8 mm, of holotype LACMIP 16655.23, LACMIP Type 12375, LACMIP Locality 16655 [=LACMIP Locality 41563; ex CSUN Locality 1563]. M–N, Juncal Formation, Canton Canyon, Whitaker Peak area, Ventura County, southern California. Basal (M) and dorsal (N) views, both 2.4x, length 19.4 mm, width 13.9, height 9.4 mm, of hypotype LACMIP 40807.1, LACMIP Type 14935 (LACMIP Locality 40807 [= LACMIP Locality 16191, ex CSUN Locality 807]). O–Q, Subepona leahae n. sp., Llajas Formation (Eocene, "Domengine Stage"), north side Simi Valley, Ventura County, southern California. Basal (O), dorsal (P), and left (labral) side (Q) views, 1.6x, length 29.5 mm, width 13.9, height 15.1 mm, of holotype LACMIP 40374.79, LACMIP Type 14936, (LACMIP Locality 40374).
Figure 2 in Revision of northeast Pacific Paleogene cypraeoidean gastropods, including recognition of three new species: implications for paleobiogeographic distribution and faunal turnover
Figure 2. Illustrations of key morphologic terms used in describing cypraeoidean shells. A=Bernaya sp., hypotype LACMIP 22341.1, type 13644; B = Protocypraea? simiensis (Nelson, 1925), holotype UCMP 30498; C = Subepona goedertorum (Groves and Squires, 1995), holotype LACMIP 16655.23, type 12375; D = Propustularia kemperae (Nelson, 1925), holotype CASG 391.01.
Table 1 in Revision of northeast Pacific Paleogene cypraeoidean gastropods, including recognition of three new species: implications for paleobiogeographic distribution and faunal turnover
<p><b>Table 1.</b> Paleogene cypraeoideans from NEP, with author(s), families, subfamilies, geographic distribution, and stage range. Taxa arranged following Lorenz (2017) and Fehse (2021) and listed alphabetically under each genus. Van Is=Vancouver Island, British Columbia, WA=Washington, OR=Oregon, CA=California, BCS Méx= Baja California Sur, México. No=North, So=South, mid=middle, n. comb.=new combination, n. sp.=new species, sp.=species.</p><table><tbody><tr><th>TAXON</th><th><b>LOCATION</b></th><th>NEP "STAGE"</th><th><b>STANDARD STAGE</b></th></tr><tr><th><b>CYPRAEIDAE</b></th></tr></tbody><tbody><tr><th><i>Nucleolaria cowlitziana</i> Groves, 1994</th><td>WA</td><td>upper "Tejon"</td><td>upper Bartonian</td></tr><tr><th><i>Propustularia kemperae</i> (Nelson, 1925)</th><td>So CA</td><td>"Martinez"</td><td>Selandian</td></tr><tr><th><i>Subepona goedertorum</i> (Groves and Squires, 1995)</th><td>WA, So CA</td><td>"Capay" to "Domengine"</td><td>mid to up Ypresian</td></tr><tr><th><i>Subepona leahae</i> Squires and Groves, n. sp.</th><td>So CA</td><td>"Domengine"</td><td>up. Ypres.-low. Lut.</td></tr><tr><th><i>Bernaya grovesi</i> Squires and Demetrion, 1992</th><td>WA?, BC Méx</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>Bernaya kaylinae</i> Squires and Groves, n. sp.</th><td>So CA</td><td>"Domengine"</td><td>up. Ypres.-low. Lut.</td></tr><tr><th><i>Bernaya squiresi</i> Groves, 2011</th><td>WA</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>Bernaya</i> sp.</th><td>No CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th><i>Protocypraea</i>? <i>simiensis</i> (Nelson, 1925) n. comb.</th><td>So CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th><i>Protocypraea</i>? sp. 1</th><td>Van Is</td><td>"Martinez"?</td><td>Thanetian?</td></tr><tr><th><i>Protocypraea</i>? sp. 2</th><td>No CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th><i>Gisortia clarki</i> Ingram, 1940</th><td>CA, BCS Méx?</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>Gisortia</i> sp.</th><td>So CA</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th>Cypraeidae, gen. and sp. indeterminate</th><td>Mid CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th><b>EOCYPRAEIDAE</b></th></tr><tr><th><i>Eocypraea batequensis</i> Groves, 2011</th><td>BCS Méx</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>Eocypraea crescentensis</i> Groves, 2011</th><td>WA</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>Eocypraea jimgoerderti</i> Groves, 2011</th><td>WA</td><td>"Trans." to "Tejon"</td><td>middle Lutetian</td></tr><tr><th><i>Eocypraea judithsmithae</i> Squires and Groves, n. sp.</th><td>So to mid CA</td><td>"Domengine."</td><td>up. Ypres.-low. Lut.</td></tr><tr><th><i>Eocypraea novasumma</i> (Nelson, 1925)</th><td>So CA, BC Méx</td><td>"Martinez"</td><td>Selandian</td></tr><tr><th><i>Eocypraea takeosusukii</i> Groves, 2011</th><td>No CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th><i>Eocypraea</i> sp. cf. <i>E. inflata</i> (Lamarck, 1802)</th><td>So CA</td><td>"Domengine"</td><td>upper Ypresian</td></tr><tr><th><i>Eocypraea</i> sp.</th><td>Mid CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th><i>Grovesia castacensis</i> (Stewart, 1926 [1927]) n. comb.</th><td>WA, So CA</td><td>mid "Tejon" to Galvinian</td><td>Barton.-Priabonian</td></tr><tr><th><i>Grovesia mathewsonii</i> (Gabb, 1869)</th><td>WA, OR, So CA</td><td>"Domeng." to Galvinian</td><td>up. Ypres.-Priabonian</td></tr><tr><th><i>Luponovula maniobraensis</i> (Squires & Advocate, 1986) n. comb.</th><td>So CA</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><b>PEDICULARIINAE</b></th></tr><tr><th><i>Cypraedia</i> sp.</th><td>BCS Méx</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>Cypraeogemmula warnerae</i> Effinger, 1938</th><td>WA</td><td>"Capay" to Galvinian</td><td>up. Ypres.-Priabon.</td></tr><tr><th><b>ERATOIDAE</b></th></tr><tr><th><i>Eratotrivia crescentensis</i> (Weaver and Palmer, 1922)</th><td>WA</td><td>"Capay"</td><td>middle Ypresian</td></tr><tr><th><i>NOMINA DUBIA</i></th></tr><tr><th><i>"</i> <i>Bernaya" fresnoensis</i> (Anderson, 1905)</th><td>mid CA</td><td>"Domengine"</td><td>up. Ypres.-low. Lut.</td></tr><tr><th><i>"</i> <i>Eocypraea" bayerquei</i> (Gabb, 1864)</th><td>No CA</td><td>Martinez?</td><td>Paleocene</td></tr><tr><th>" <i>Sphaerocypraea" martini</i> (Dickerson, 1914)</th><td>No CA</td><td>"Martinez"</td><td>Thanetian</td></tr><tr><th>" <i>Sulcocypraea" oakvillensis</i> (Van Winkle, 1918)</th><td>WA</td><td>lower Galvinian</td><td>lower Priabonian</td></tr></tbody></table>
Figure 1 in Revision of northeast Pacific Paleogene cypraeoidean gastropods, including recognition of three new species: implications for paleobiogeographic distribution and faunal turnover
Figure 1. Index map of the northeast Pacific (NEP) region with latitudinal ranges of cypraeoidean species discussed in this present study, excluding nomina dubia.
Figure 3 in Revision of northeast Pacific Paleogene cypraeoidean gastropods, including recognition of three new species: implications for paleobiogeographic distribution and faunal turnover
Figure 3. Chronostratigraphic diagram showing all the known NEP cypraeoidean genera, their key stratigraphic units, number of identifiable genera, and global-climate events. Geologic time scale, stage ages, chrons/polarity, nannofossil zones, and timing of global-climate events from Gradstein et al. (2012: fig. 28.11). Provincial- molluscan stages from Squires (2003: fig. 21.). Geologic age of "Stewart bed" from Squires (2022: fig. 3).
An ecosystem sentinel for the northeast Pacific Ocean twilight zone
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Data from: Convergent evolution of niche structure in Northeast Pacific kelp forests
<ol> <li>Much of the morphological and ecological diversity present on earth is believed to have arisen through the process of adaptive radiation. Yet, this is seemingly at odds with substantial evidence that niches tend to be similar among closely related species (i.e., niche conservatism). Identifying the relative importance of these opposing processes in driving niche evolution under different circumstances is therefore essential to our understanding of the interaction between ecological and evolutionary phenomena.</li> <li>In this study, we make use of recent advances in our understanding of the phylogeny of kelps (Laminariales) to investigate niche evolution in one of the most ecologically significant groups of benthic habitat-forming organisms on the planet. We quantify functional traits and use community sampling data from a kelp diversity hotspot to determine which traits are responsible for the habitat (β) niche of kelps and whether they are labile or conserved across the kelp phylogeny. </li> <li>We find that combinations of functional traits have evolved convergently across kelp subclades and that these functional traits are significant predictors of community structure. Specifically, traits associated with whole-kelp structural reinforcement and material properties were found to be significantly correlated with species distributions along a gradient of wave disturbance and thus predict the outcome of environmental filtering. However, kelp assemblages were made up of species that are more phylogenetically distinct than expected (i.e., phylogenetic overdispersion), suggesting that niche partitioning along this gradient of wave disturbance has been an important driver of divergence between close relatives.</li> <li>These results are consistent with the hypothesis that environmental filtering associated with wave disturbance plays an essential role in determining the habitat niche of kelps across local communities and further suggest that this process can drive phenotypic divergence and niche partitioning between close relatives. We propose that parallel adaptive radiation of kelp subclades has shaped the diversity and species composition of kelp forests in the Northeast Pacific and we discuss how evidence from the literature on incipient or ongoing speciation events support this hypothesis.</li> </ol>
Data from: Watershed classification predicts streamflow regime and organic carbon dynamics in the Northeast Pacific Coastal Temperate Rainforest
<p class="Abstract">Watershed classification has long been a key tool in the hydrological sciences, but few studies have been extended to biogeochemistry. We developed a combined hydro-biogeochemical classification for watersheds draining to the coastal margin of the Northeast Pacific coastal temperate rainforest (1,443,062<i> </i>km<sup>2</sup>), including 2,695 small coastal rivers (SCR) and 10 large continental watersheds. We used cluster analysis to group SCR watersheds into 12 types, based on watershed properties. The most important variables for distinguishing SCR watershed types were evapotranspiration, slope, snowfall, and total precipitation. We used both streamflow and dissolved organic carbon (DOC) measurements from rivers (<i>n</i> = 104 and 90 watersheds respectively) to validate the classification. Watershed types corresponded with broad differences in streamflow regime, mean annual runoff, DOC seasonality, and mean DOC concentration. These links between watershed type and river conditions enabled the first region-wide empirical characterization of river hydro-biogeochemistry at the land-sea margin, spanning extensive ungauged and unsampled areas. We found very high annual runoff (mean > 3000 mm, <i>n</i> = 10) in three watershed types totaling 59,024 km<sup>2</sup> and ranging from heavily glacierized mountain watersheds with high flow in summer to a rain-fed mountain watershed type with high flow in fall-winter. DOC hotspots (mean > 4 mg L<sup>-1</sup>, <i>n</i> = 14) were found in three other watershed types (48,557 km<sup>2</sup>) with perhumid rainforest climates and less-mountainous topography. We described four patterns of DOC seasonality linked to watershed hydrology, with fall-flushing being widespread. Hydro-biogeochemical watershed classification may be useful for other complex regions with sparse observation networks.</p>
Data and Code: Detecting Blue Whale Calls in the Northeast Pacific Using Seismic Systems (Undergraduate Thesis)
<p><strong>SeismoData.ipynb</strong>: This Jupyter notebook is adapted from seismosocialdistancing.ipynb created by Thomas Lecocq, Fred Massin and Claudio Satriano. SeismoData.ipynb was used to retrieve seismic waveform data from the Incorporated Research Institutions for Seismology (IRIS) Data Management Center (DMC) (https://ds.iris.edu/ds/ nodes/dmc/) and convert files from miniSEED to SAC format. It was also used to preview waveform and spectrogram plots.</p> <p><strong>BlueWhaleDetectionResults_J53A_Dec132011.mat</strong>: This .mat file summarizes whale detection results from OBS J53A on December 13th 2011. The objective was to calibrate a detection algoritm created for Northwest Atlantic blue whale A calls by Plourde and Nedimovic (2022), so that it can target Northeast Pacific blue whale B calls using seismometers off Washington and California. Three tests were performed to find optimal parameters. <em>BlueWhaleDetections_J53A_Test1</em><strong> </strong>are the detection results of a control that uses Northwest Atlantic blue whale parameters (16.25-18Hz frequency and 68-78s period ranges). <em>BlueWhaleDetections_J53A_Test2</em> <strong> </strong>are the detection results using Northeast Pacific blue whale B call parameters (14-17Hz frequency and 45-55s period ranges). <em>BlueWhaleDetections_J53A_Test2 </em>are the detection results using Northeast Pacific blue whale B call and C call parameters (10.5-12Hz and 14-17Hz frequency and 45-55s period ranges). <em>BlueWhaleDetections_J53A_SCC</em> are the 95% probability detection results from the Wilcock and Hilmo (2021) blue whale catalogue created using spectrogram cross-correlation. </p> <p><strong>NEPBlueWhaleMATLABcodes.zip</strong>: Contains scripts to run the recurrence interval power ratio method created by Plourde and Nedimovic (2022), adjusted to detect Northeast Pacific blue whale B calls and plot waveforms/spectrograms. First run <em>DetectBlueWhales.m </em>to calculate the recurrence power ratio every 12 minutes, then run C<em>reateBlueWhaleDetectionList.m </em>to classify detections with high power ratios and likely blue whale call detections.</p> <p><strong>BlueWhaleDetectionResults_CapeMendocino_Dec15to292014.mat</strong>: This .mat file summarizes the blue whale detection results from 2 OBS (FS02D and FS07D) and 1 land seismometer (CM09A) in close proximity, using Test 2 parameters. Note if there are less than 3 BWD in a given day, these are likely false detections.</p>
Species counts, depth and latitude from NOAA's annual groundfish trawl surveys (1999-2018) in the Northeast Pacific
<p>These data are provided as Supporting Information to the article appearing in Ecology Letters entitled: "Non-linear models of species' responses to environmental and spatial gradients".</p> <p>The article describes a parametric framework for modelling species-environment non-linear relationships, including an R package ('<em>senlm</em>'), available on Github: <a href="https://primer-e.github.io/senlm">https://primer-e.github.io/senlm</a>. The framework has two components: (i) a non-linear parametric mathematical function to model the mean species response along a gradient that allows asymmetry, flattening/peakedness or bimodality; and (ii) a statistical error distribution tailored for ecological data types, allowing intrinsic mean-variance relationships and zero-inflation. The article demonstrates the utility of this model framework, highlighting the flexibility of a range of possible mean functions and a broad range of potential error distributions, in analyses of fish species' abundances along a depth gradient, and how they change over time and at different latitudes.</p> <p>A vignette in R ('Vignette_S1.pdf') and associated R code ('Rcode_S1.txt') that utilise this dataset to demonstrate the <em>senlm</em> modeling framework are available as Supporting Information to the article.</p>
Genomic diversity gradients and functional differentiation put Northeast Pacific ribbon kelp lineages in the speciation grey zone
<p><span>The transition from reproductively isolated populations to species is not well understood. Genotyping entire genomes holds promise to enhance insights into the process of speciation and the evolutionary relationships among related taxa. Gulf of Alaska ribbon kelp was once recognized as four species before they were folded into <em>Alaria</em> <em>marginata</em> on the basis of DNA barcode markers, though several lineages have continued to be recognized. Here, we used whole genome sequencing datasets to test the hypothesis that these lineages represent incipient species. Whole genomes of 69 individuals from five genetically distinctive lineages in the Gulf of Alaska (USA) and Salish Sea (Canada) were analyzed, along with 63 genomes from three other species of <em>Alaria</em>. Our analysis of >3.4 million Single Nucleotide Polymorphisms reaffirms that organellar and nuclear phylogenetic signals are incongruent in <em>Alaria</em>, producing different topologies among five organellar and six nuclear <em>A</em>. <em>marginata</em> lineages. Lineages also display reproductive isolation, evidenced by a lack of recent admixture across genomes. Genetic distances between <em>A</em>. <em>marginata</em> lineages exceed levels expected of population-level divergence but fall short of distances between species of <em>Alaria</em>. Moreover, we provide evidence of functional genomic differences between the <em>A</em>. <em>marginata</em> lineages, exceeding differences expected between populations, but falling short of larger differences among species. Our results place <em>A</em>. <em>marginata</em> lineages in an evolutionary grey zone, where lineages display substantial differentiation, but not to the level expected of <em>Alaria</em> species. This information shifts taxonomic conversations towards a genome-scale framework that provides a more comprehensive picture of divergence, connectivity, and functional innovation for defining lineages.</span></p>
Data from: Watershed classification predicts streamflow regime and organic carbon dynamics in the Northeast Pacific Coastal Temperate Rainforest
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Data from: Convergent evolution of niche structure in Northeast Pacific kelp forests
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Data from:The foe you know: Observations of interspecific interactions between small cetaceans and northern resident killer whales (Orcinus orca) in the northeast Pacific
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Dataset: Spatiotemporal patterns of salmon winter habitat usage in the Northeast Pacific uncovered by environmental DNA
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Species counts, depth and latitude from NOAA's annual groundfish trawl surveys (1999-2018) in the Northeast Pacific
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Genomic diversity gradients and functional differentiation put Northeast Pacific ribbon kelp lineages in the speciation grey zone
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Data from: Long-term tracking captures the timing of ontogenetic niche shifts in Northeast Pacific white sharks
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Data: Near-bottom currents at Station M in the abyssal Northeast Pacific
<p>Current meter data collected by the Monterey Bay Aquarium Research Institute (MBARI) at Station M, located on the abyssal plain 220 km offshore of central California. Collected near the seabed at ~4000 m depth from October 2014–October 2018. Data and methods are described in the publication:</p> <p>Connolly, T. P., P. R. McGill, R. G. Henthorn, D. A. Burrier, C. Michaud, Near-bottom currents at Station M in the abyssal Northeast Pacific, <em>submitted to Deep Sea Research II</em></p> <p><strong>Data files</strong></p> <p>Each .zip folder contains a readme.txt file describing the data files.</p> <p><em>ADCP.zip</em> - contains data from a one-year Acoustic Doppler Current Profiler (ADCP) deployment. Includes the binary file uploaded from the instrument and a text file created using RDI tools.</p> <p><em>ADCP_netcdf.zip</em> - contains processed ADCP data in NetCDF format.</p> <p><em>Rover_merged.zip</em> - contains merged data files from four years of benthic rover current meter deployments, in Excel .xlsx format and comma-separated value .csv format.</p> <p><strong>Analysis code</strong></p> <p>Analysis code is available at <a href="https://github.com/tompc35/station-m-currents">https://github.com/tompc35/station-m-currents</a></p>
Data from Jenkinson et al. 2020: Biogeographical variation in the distribution, abundance, and interactions among key species on rocky reefs of the northeast Pacific
<p>See Metadata tab for full description of transect survey data.</p>
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