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  • Proceedings of the National Academy of Sciences  (40)
  • 2020-2024  (40)
  • Biology  (40)
  • 11
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    The Earth BioGenome Project 2020: Starting the clock
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 4 ( 2022-01-25)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 4 ( 2022-01-25)
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    URL: Article
    DOI: 10.1073/pnas.2115635118
    DOI: 10.37473/fic/10.1073/pnas.2115635118
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 12
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    Evolution of the ancestral mammalian karyotype and syntenic regions
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 40 ( 2022-10-04)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 40 ( 2022-10-04)
    Abstract: Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2209139119
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
    detail.hit.zdb_id: 209104-5
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  • 13
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    Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 44 ( 2022-11)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 44 ( 2022-11)
    Abstract: This study explores how researchers’ analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers’ expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each team’s workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers’ results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2203150119
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
    detail.hit.zdb_id: 209104-5
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  • 14
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    Country-level gender inequality is associated with structural differences in the brains of women and men
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 20 ( 2023-05-16)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 20 ( 2023-05-16)
    Abstract: Gender inequality across the world has been associated with a higher risk to mental health problems and lower academic achievement in women compared to men. We also know that the brain is shaped by nurturing and adverse socio-environmental experiences. Therefore, unequal exposure to harsher conditions for women compared to men in gender-unequal countries might be reflected in differences in their brain structure, and this could be the neural mechanism partly explaining women’s worse outcomes in gender-unequal countries. We examined this through a random-effects meta-analysis on cortical thickness and surface area differences between adult healthy men and women, including a meta-regression in which country-level gender inequality acted as an explanatory variable for the observed differences. A total of 139 samples from 29 different countries, totaling 7,876 MRI scans, were included. Thickness of the right hemisphere, and particularly the right caudal anterior cingulate, right medial orbitofrontal, and left lateral occipital cortex, presented no differences or even thicker regional cortices in women compared to men in gender-equal countries, reversing to thinner cortices in countries with greater gender inequality. These results point to the potentially hazardous effect of gender inequality on women’s brains and provide initial evidence for neuroscience-informed policies for gender equality.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2218782120
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
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  • 15
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    Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 20 ( 2022-05-17)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 20 ( 2022-05-17)
    Abstract: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus , and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel ( 〉 300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2117440119
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 16
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    Global airborne sampling reveals a previously unobserved dimethyl sulfide oxidation mechanism in the marine atmosphere
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 9 ( 2020-03-03), p. 4505-4510
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 9 ( 2020-03-03), p. 4505-4510
    Abstract: Dimethyl sulfide (DMS), emitted from the oceans, is the most abundant biological source of sulfur to the marine atmosphere. Atmospheric DMS is oxidized to condensable products that form secondary aerosols that affect Earth’s radiative balance by scattering solar radiation and serving as cloud condensation nuclei. We report the atmospheric discovery of a previously unquantified DMS oxidation product, hydroperoxymethyl thioformate (HPMTF, HOOCH 2 SCHO), identified through global-scale airborne observations that demonstrate it to be a major reservoir of marine sulfur. Observationally constrained model results show that more than 30% of oceanic DMS emitted to the atmosphere forms HPMTF. Coincident particle measurements suggest a strong link between HPMTF concentration and new particle formation and growth. Analyses of these observations show that HPMTF chemistry must be included in atmospheric models to improve representation of key linkages between the biogeochemistry of the ocean, marine aerosol formation and growth, and their combined effects on climate.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1919344117
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
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  • 17
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    Local- and regional-scale racial and ethnic disparities in air pollution determined by long-term mobile monitoring
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 37 ( 2021-09-14)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 37 ( 2021-09-14)
    Abstract: Disparity in air pollution exposure arises from variation at multiple spatial scales: along urban-to-rural gradients, between individual cities within a metropolitan region, within individual neighborhoods, and between city blocks. Here, we improve on existing capabilities to systematically compare urban variation at several scales, from hyperlocal ( 〈 100 m) to regional ( 〉 10 km), and to assess consequences for outdoor air pollution experienced by residents of different races and ethnicities, by creating a set of uniquely extensive and high-resolution observations of spatially variable pollutants: NO, NO 2 , black carbon (BC), and ultrafine particles (UFP). We conducted full-coverage monitoring of a wide sample of urban and suburban neighborhoods (93 km 2 and 450,000 residents) in four counties of the San Francisco Bay Area using Google Street View cars equipped with the Aclima mobile platform. Comparing scales of variation across the sampled population, greater differences arise from localized pollution gradients for BC and NO (pollutants dominated by primary sources) and from regional gradients for UFP and NO 2 (pollutants dominated by secondary contributions). Median concentrations of UFP, NO, and NO 2 are, for Hispanic and Black populations, 8 to 30% higher than the population average; for White populations, average exposures to these pollutants are 9 to 14% lower than the population average. Systematic racial/ethnic disparities are influenced by regional concentration gradients due to sharp contrasts in demographic composition among cities and urban districts, while within-group extremes arise from local peaks. Our results illustrate how detailed and extensive fine-scale pollution observations can add new insights about differences and disparities in air pollution exposures at the population scale.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2109249118
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
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  • 18
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    The influence of iodine on the Antarctic stratospheric ozone hole
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 7 ( 2022-02-15)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 7 ( 2022-02-15)
    Abstract: The catalytic depletion of Antarctic stratospheric ozone is linked to anthropogenic emissions of chlorine and bromine. Despite its larger ozone-depleting efficiency, the contribution of ocean-emitted iodine to ozone hole chemistry has not been evaluated, due to the negligible iodine levels previously reported to reach the stratosphere. Based on the recently observed range (0.77 ± 0.1 parts per trillion by volume [pptv]) of stratospheric iodine injection, we use the Whole Atmosphere Community Climate Model to assess the role of iodine in the formation and recent past evolution of the Antarctic ozone hole. Our 1980–2015 simulations indicate that iodine can significantly impact the lower part of the Antarctic ozone hole, contributing, on average, 10% of the lower stratospheric ozone loss during spring (up to 4.2% of the total stratospheric column). We find that the inclusion of iodine advances the beginning and delays the closure stages of the ozone hole by 3 d to 5 d, increasing its area and mass deficit by 11% and 20%, respectively. Despite being present in much smaller amounts, and due to faster gas-phase photochemical reactivation, iodine can dominate (∼73%) the halogen-mediated lower stratospheric ozone loss during summer and early fall, when the heterogeneous reactivation of inorganic chlorine and bromine reservoirs is reduced. The stratospheric ozone destruction caused by 0.77 pptv of iodine over Antarctica is equivalent to that of 3.1 (4.6) pptv of biogenic very short-lived bromocarbons during spring (rest of sunlit period). The relative contribution of iodine to future stratospheric ozone loss is likely to increase as anthropogenic chlorine and bromine emissions decline following the Montreal Protocol.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2110864119
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 19
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    Six hundred years of South American tree rings reveal an increase in severe hydroclimatic events since mid-20th century
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 29 ( 2020-07-21), p. 16816-16823
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 29 ( 2020-07-21), p. 16816-16823
    Abstract: South American (SA) societies are highly vulnerable to droughts and pluvials, but lack of long-term climate observations severely limits our understanding of the global processes driving climatic variability in the region. The number and quality of SA climate-sensitive tree ring chronologies have significantly increased in recent decades, now providing a robust network of 286 records for characterizing hydroclimate variability since 1400 CE. We combine this network with a self-calibrated Palmer Drought Severity Index (scPDSI) dataset to derive the South American Drought Atlas (SADA) over the continent south of 12°S. The gridded annual reconstruction of austral summer scPDSI is the most spatially complete estimate of SA hydroclimate to date, and well matches past historical dry/wet events. Relating the SADA to the Australia–New Zealand Drought Atlas, sea surface temperatures and atmospheric pressure fields, we determine that the El Niño–Southern Oscillation (ENSO) and the Southern Annular Mode (SAM) are strongly associated with spatially extended droughts and pluvials over the SADA domain during the past several centuries. SADA also exhibits more extended severe droughts and extreme pluvials since the mid-20th century. Extensive droughts are consistent with the observed 20th-century trend toward positive SAM anomalies concomitant with the weakening of midlatitude Westerlies, while low-level moisture transport intensified by global warming has favored extreme rainfall across the subtropics. The SADA thus provides a long-term context for observed hydroclimatic changes and for 21st-century Intergovernmental Panel on Climate Change (IPCC) projections that suggest SA will experience more frequent/severe droughts and rainfall events as a consequence of increasing greenhouse gas emissions.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2002411117
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
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  • 20
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    Photocatalytic chlorine atom production on mineral dust–sea spray aerosols over the North Atlantic
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 31 ( 2023-08)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 31 ( 2023-08)
    Abstract: Active chlorine in the atmosphere is poorly constrained and so is its role in the oxidation of the potent greenhouse gas methane, causing uncertainty in global methane budgets. We propose a photocatalytic mechanism for chlorine atom production that occurs when Sahara dust mixes with sea spray aerosol. The mechanism is validated by implementation in a global atmospheric model and thereby explaining the episodic, seasonal, and location-dependent 13 C depletion in CO in air samples from Barbados [J.E. Mak, G. Kra, T. Sandomenico, P. Bergamaschi, J. Geophys. Res. Atmos. 108 (2003)], which remained unexplained for decades. The production of Cl can also explain the anomaly in the CO:ethane ratio found at Cape Verde [K. A. Read et al., J. Geophys. Res. Atmos. 114 (2009)], in addition to explaining the observation of elevated HOCl [M. J. Lawler et al., Atmos. Chem. Phys. 11 , 7617–7628 (2011)]. Our model finds that 3.8 Tg(Cl) y −1 is produced over the North Atlantic, making it the dominant source of chlorine in the region; globally, chlorine production increases by 41%. The shift in the methane sink budget due to the increased role of Cl means that isotope-constrained top–down models fail to allocate 12 Tg y −1 (2% of total methane emissions) to 13 C-depleted biological sources such as agriculture and wetlands. Since 2014, an increase in North African dust emissions has increased the 13 C isotope of atmospheric CH 4 , thereby partially masking a much greater decline in this isotope, which has implications for the interpretation of the drivers behind the recent increase of methane in the atmosphere.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2303974120
    RVK:
    TA 1000
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
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