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Open Access Publications from the University of California

Scholarly Works (213 results)

  • Article
  • Peer Reviewed
Biogeographia – The Journal of Integrative Biogeography, Volume 11 (1987)
    Cover page: Modelli di distribuzione dell'entomofauna della Zona di Transizione Cinese, analisi di esempi e ipotesi sulle origini
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2017)

    The influence of the lunar cycle on dolphin foraging behavior was investigated in the productive, southern California Current Ecosystem and the oligotrophic Hawaiian Archipelago. Passive acoustic recordings from 2009 to 2015 were analyzed to document the presence of echolocation from four dolphin species that demonstrate distinct foraging preferences and diving abilities. Visual observations of dolphins, cloud coverage, commercial landings of market squid (Doryteuthis opalescens) and acoustic backscatter of fish were also considered in the Southern California Bight. The temporal variability of echolocation is described from daily to annual timescales, with emphasis on the lunar cycle as an established behavioral driver for potential dolphin prey. For dolphins that foraged at night, the presence of echolocation was reduced during nights of the full moon and during times of night that the moon was present in the night sky. In the Southern California Bight, echolocation activity was reduced for both shallow- diving common dolphins (Delphinus delphis) and deeper-diving Risso’s dolphins (Grampus griseus) during times of increased illumination. Seasonal differences in acoustic behavior for both species suggest a geographic shift in dolphin populations, shoaling scattering layers or prey switching behavior during warm months, whereby dolphins target prey that do not vertically migrate. In the Hawaiian Archipelago, deep-diving short-finned pilot whales (Globicephala macrorhynchus) and shallow-diving false killer whales (Pseudorca crassidens) also showed reduced echolocation behavior during periods of increased lunar illumination. In contrast to nocturnal foraging in the northwestern Hawaiian Islands, false killer whales in the main Hawaiian Islands mainly foraged during the day and the lunar cycle showed little influence on their nocturnal acoustic behavior. Different temporal patterns in false killer whale acoustic behavior between the main and northwestern Hawaiian Islands can likely be attributed to the presence of distinct populations or social clusters with dissimilar foraging strategies. Consistent observations of reduced acoustic activity during times of increased lunar illumination show that the lunar cycle is an important predictor for nocturnal dolphin foraging behavior. The result of this research advances the scientific understanding of how dolphins optimize their foraging behavior in response to the changing distribution and abundance of their prey.

      Cover page: By the Light of the Moon: North Pacific Dolphins Optimize Foraging with the Lunar Cycle
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2013)
        Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2017)
        In the Southern California Bight, the common dolphin Delphinus delphis is the most abundant dolphin species and preys upon small pelagic fish, mesopelagic fish, and cephalopods. Mesopelagic fish and many cephalopods are available throughout the year, and they form deep scattering layers, some of which characteristically undergo strong diel vertical migrations. The extent of vertical migration depends on the degree of sea surface solar and lunar illumination. At their daytime depth, mesopelagic prey are beyond the range of shallow-diving dolphins. Autonomous acoustic recorders were used tomonitor dolphin echolocation at 2 offshore recording locations from 2009 to 2014. Manual and automated classification techniques were used to identify periods of high echolocation activity, indicative of common dolphin foraging. Clear lunar patterns existed in cool months, when echolocation activity was highest during the darkest periods of the night and lunar month, indicating times when dolphins were foraging, possibly on mesopelagic prey. Echolocation was more abundant during warmmonths, but diel and lunar patterns in echolocation were weaker. Generalized additive mixed models show that the observed patterns in echolocation activity are correlated with lunar day and position of the moon in the night sky. Seasonal patterns may represent geographic shifts in common dolphin populations, shoaling scattering layers, or prey switching behavior during the warmmonths, whereby dolphins target small pelagic fish not associated with the deep scattering layers. Overall, dolphin foraging activity declined from 2009 to 2014 during warm months, which may be related to a declining abundance of small pelagic fish.
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2014)
          At least ten species of beaked whales inhabit the North Pacific, but little is known about their abundance, ecology, and behavior, as they are elusive and difficult to distinguish visually at sea. Six of these species produce known species-specific frequency modulated (FM) echolocation pulses: Baird's, Blainville's, Cuvier's, Deraniyagala's, Longman's, and Stejneger's beaked whales. Additionally, one described FM pulse (BWC) from Cross Seamount, Hawai'i, and three unknown FM pulse types (BW40, BW43, BW70) have been identified from almost 11 cumulative years of autonomous recordings at 24 sites throughout the North Pacific. Most sites had a dominant FM pulse type with other types being either absent or limited. There was not a strong seasonal influence on the occurrence of these signals at any site, but longer time series may reveal smaller, consistent fluctuations. Only the species producing BWC signals, detected throughout the Pacific Islands region, consistently showed a diel cycle with nocturnal foraging. By comparing stranding and sighting information with acoustic findings, we hypothesize that BWC signals are produced by ginkgo-toothed beaked whales. BW43 signal encounters were restricted to Southern California and may be produced by Perrin's beaked whale, known only from Californian waters. BW70 signals were detected in the southern Gulf of California, which is prime habitat for Pygmy beaked whales. Hubb's beaked whale may have produced the BW40 signals encountered off central and southern California; however, these signals were also recorded off Pearl and Hermes Reef and Wake Atoll, which are well south of their known range.
            Cover page: Spatio-Temporal Patterns of Beaked Whale Echolocation Signals in the North Pacific
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2012)
            Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described. In contrast, de novo gene birth remains poorly understood, mainly because translation of sequences devoid of genes, or 'non-genic' sequences, is expected to produce insignificant polypeptides rather than proteins with specific biological functions. Here we formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes generated by widespread translational activity in non-genic sequences. Testing this model at the genome scale in Saccharomyces cerevisiae, we detect translation of hundreds of short species-specific open reading frames (ORFs) located in non-genic sequences. These translation events seem to provide adaptive potential, as suggested by their differential regulation upon stress and by signatures of retention by natural selection. In line with our model, we establish that S. cerevisiae ORFs can be placed within an evolutionary continuum ranging from non-genic sequences to genes. We identify ~1,900 candidate proto-genes among S. cerevisiae ORFs and find that de novo gene birth from such a reservoir may be more prevalent than sporadic gene duplication. Our work illustrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation.
              Cover page: Proto-genes and de novo gene birth
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2013)
              Beaked whale echolocation signals are mostly frequency-modulated (FM) upsweep pulses and appear to be species specific. Evolutionary processes of niche separation may have driven differentiation of beaked whale signals used for spatial orientation and foraging. FM pulses of eight species of beaked whales were identified, as well as five distinct pulse types of unknown species, but presumed to be from beaked whales. Current evidence suggests these five distinct but unidentified FM pulse types are also species-specific and are each produced by a separate species. There may be a relationship between adult body length and center frequency with smaller whales producing higher frequency signals. This could be due to anatomical and physiological restraints or it could be an evolutionary adaption for detection of smaller prey for smaller whales with higher resolution using higher frequencies. The disadvantage of higher frequencies is a shorter detection range. Whales echolocating with the highest frequencies, or broadband, likely lower source level signals also use a higher repetition rate, which might compensate for the shorter detection range. Habitat modeling with acoustic detections should give further insights into how niches and prey may have shaped species-specific FM pulse types.
                • Article
                • Peer Reviewed
                LBL Publications (2016)
                The calcium isotopes have emerged as an important testing ground for new microscopically derived shell-model interactions, and a great deal of focus has been directed toward this region. We investigate the relative spectroscopic strengths associated with $1f_{7/2}$ neutron hole states in $^{47, 49}$Ca following one-neutron knockout reactions from $^{48,50}$Ca. The observed reduction of strength populating the lowest 7/2$^{-}_{1}$ state in $^{49}$Ca, as compared to $^{47}$Ca, is consistent with the description given by shell-model calculations based on two- and three-nucleon forces in the neutron $pf$ model space, implying a fragmentation of the $l$=3 strength to higher-lying states. The experimental result is inconsistent with both the GXPF1 interaction routinely used in this region of the nuclear chart and with microscopic calculations in an extended model space including the $ u1g_{9/2}$ orbital.
                  Cover page: Unexpected distribution of $ u1f_{7/2}$ strength in the calcium isotopes at $N$=30
                  • Article
                  • Peer Reviewed
                  LBL Publications (2017)
                  The calcium isotopes have emerged as a critical testing ground for new microscopically derived shell-model interactions, and a great deal of experimental and theoretical focus has been directed toward this region. We investigate the relative spectroscopic strengths associated with 1f7/2 neutron hole states in Ca47,49 following one-neutron knockout reactions from Ca48,50. The observed reduction of strength populating the 7/21- state in Ca49, as compared to Ca47, is inconsistent with shell-model calculations using both phenomenological interactions such as GXPF1, and interactions derived from microscopically based two- and three-nucleon forces. The result suggests a fragmentation of the l=3 strength to higher-lying states as suggested by the microscopic calculations, but the observed magnitude of the reduction is not reproduced in any shell-model description.
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2017)
                    The cross section of top quark-antiquark pair production in proton-proton collisions at [Formula: see text] is measured by the CMS experiment at the LHC, using data corresponding to an integrated luminosity of 2.2[Formula: see text]. The measurement is performed by analyzing events in which the final state includes one electron, one muon, and two or more jets, at least one of which is identified as originating from hadronization of a b quark. The measured cross section is [Formula: see text], in agreement with the expectation from the standard model.
                      Cover page: Measurement of the tt¯ production cross section using events in the eμ final state in pp collisions at s=13TeV
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