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1. Early, intensive marine resource exploitation by Middle Stone Age humans at Ysterfontein 1 rockshelter, South Africa

   https://doi.org/10.1073/pnas.2020042118  

   Niespolo, Elizabeth M.; Sharp, Warren D.; Avery, Graham; Dawson, Todd E. (April 2021, Proceedings of the National Academy of Sciences)

   Modern human behavioral innovations from the Middle Stone Age (MSA) include the earliest indicators of full coastal adaptation evidenced by shell middens, yet many MSA middens remain poorly dated. We apply²³⁰Th/U burial dating to ostrich eggshells (OES) from Ysterfontein 1 (YFT1, Western Cape, South Africa), a stratified MSA shell midden.²³⁰Th/U burial ages of YFT1 OES are relatively precise (median ± 2.7%), consistent with other age constraints, and preserve stratigraphic principles. Bayesian age–depth modeling indicates YFT1 was deposited between 119.9 to 113.1 thousand years ago (ka) (95% CI of model ages), and the entire 3.8 m thick midden may have accumulated within ∼2,300 y. Stable carbon, nitrogen, and oxygen isotopes of OES indicate that during occupation the local environment was dominated by C₃vegetation and was initially significantly wetter than at present but became drier and cooler with time. Integrating archaeological evidence with OES²³⁰Th/U ages and stable isotopes shows the following: 1) YFT1 is the oldest shell midden known, providing minimum constraints on full coastal adaptation by ∼120 ka; 2) despite rapid sea-level drop and other climatic changes during occupation, relative shellfish proportions and sizes remain similar, suggesting adaptive foraging along a changing coastline; 3) the YFT1 lithic technocomplex is similar to other west coast assemblages but distinct from potentially synchronous industries along the southern African coast, suggesting human populations were fragmented between seasonal rainfall zones; and 4) accumulation rates (up to 1.8 m/ka) are much higher than previously observed for dated, stratified MSA middens, implying more intense site occupation akin to Later Stone Age middens. 

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2. Transformative Impacts of Sea-Level Rise, Storm Surge, and Wetland Migration on Intertidal Native Shell-Bearing Sites in Florida’s Largest Open-Water Estuary, Tampa Bay, Florida, USA

   https://doi.org/10.1007/s12237-024-01329-8  

   Rogers, Jaime A.; Jackson, Kendal (February 2024, Estuaries and Coasts)

   Although shell middens and mounds often occupy the same intertidal spaces as coastal wetlands, biophysical interactions between these cultural features and wetlands are under-investigated. To this end, our geoarchaeological and zooarchaeological research at three coastal archaeological sites within the Tampa Bay Estuary, USA, sought to understand the interactions between shell-bearing sites, sea-level rise, storms, and migrating wetland habitats. Percussion core transects document the accretion of mangrove peat atop intact shell midden, illustrating the ability of mangrove forests to encroach shell midden and preserve cultural material below. Landward wetland deposits are thicker and muddier than those along the seaward margin of the sites, suggesting that shell-bearing sites attenuate wave energy much like other shoreline stabilization structures. Differences in sedimentology, stratigraphy, and invertebrate species compositions highlight the variability in storm impacts between sites. Storm-driven depositional events are identified by medium-to-fine sand beds with high densities of fragmented shell and small intertidal zone snails. Geospatial analyses indicate that wetland encroachment is already occurring at 247 archaeological sites within the Tampa Bay Estuary. Approximately 100 additional archaeological sites currently located in upland habitats may provide topographic relief for migrating coastal wetlands in the future. We contend that shell middens and mounds constructed by Indigenous peoples are important components within estuarine mosaics, as they have been for millennia. We advocate for further collaboration between archaeologists and estuary managers and the inclusion of descendant communities to co-manage the future of their past. 

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3. Compilation of a database of Holocene nearshore marine mollusk shell geochemistry from the California Current System

   https://doi.org/10.5194/essd-14-1695-2022  

   Palmer, Hannah M.; Padilla Vriesman, Veronica; Banker, Roxanne M.; Bean, Jessica R. (January 2022, Earth System Science Data)

   Abstract. The shells of marine invertebrates can serve as high-resolution records ofoceanographic and atmospheric change through time. In particular, oxygen andcarbon isotope analyses of nearshore marine calcifiers that grow byaccretion over their lifespans provide seasonal records of environmental andoceanographic conditions. Archaeological shell middens generated byIndigenous communities along the northwest coast of North America containshells harvested over multiple seasons for millennia. These shell middens,as well as analyses of archival and modern shells, have the potential toprovide multi-site, seasonal archives of nearshore conditions throughout theHolocene. A significant volume of oxygen and carbon isotope data fromarchaeological shells exist, yet they are separately published in archaeological,geochemical, and paleoceanographic journals and have not been comprehensivelyanalyzed to examine oceanographic change over time. Here, we compiled adatabase of previously published oxygen and carbon isotope data fromarchaeological, archival, and modern marine mollusks from the CaliforniaCurrent System (North American coast of the northeast Pacific, 32 to55∘ N). This database includes oxygen and carbon isotope data from 598modern, archaeological, and sub-fossil shells from 8880 years before present(BP) to the present, from which there are 4917 total δ13C and7366 total δ18O measurements. Shell dating and samplingstrategies vary among studies (1–345 samples per shell, mean 44.7 samplesper shell) and vary significantly by journal discipline. Data are fromvarious bivalves and gastropod species, with Mytilus spp. being the most commonlyanalyzed taxon. This novel database can be used to investigate changes innearshore sea surface conditions including warm–cool oscillations, heatwaves, and upwelling intensity, and it provides nearshore calcium carbonateδ13C and δ18O values that can be compared to thevast collections of offshore foraminiferal calcium carbonate δ13C and δ18O data from marine sediment cores. Byutilizing previously published geochemical data from midden and museumshells rather than sampling new specimens, future scientific research canreduce or omit the alteration or destruction of culturally valued specimensand sites. The dataset is publicly available through PANGAEA athttps://doi.org/10.1594/PANGAEA.941373 (Palmer et al.,2021). 

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4. cis -Regulatory Elements in Plant Development, Adaptation, and Evolution

   https://doi.org/10.1146/annurev-arplant-070122-030236  

   Marand, Alexandre P.; Eveland, Andrea L.; Kaufmann, Kerstin; Springer, Nathan M. (May 2023, Annual Review of Plant Biology)

   cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaptation. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged behind that in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes. 

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5. Spatiotemporal gene expression atlas of the extremophyte Schrenkiella parvula

   Wijesinghege, Chathura; Wang, Guannan; Pantha, Pramod; Tran, Kieu-Nga; Dassanayake, Maheshi (October 2022, bioRxiv)

   Extremophytes are naturally selected to survive environmental stresses, but scarcity of genetic resources for them developed with spatiotemporal resolution limit their use in stress biology. Schrenkiella parvula is one of the leading extremophyte models with initial molecular genomic resources developed to study its tolerance mechanisms to high salinity. Here we present a transcriptome atlas for S. parvula with subsequent analyses to highlight its diverse gene expression networks associated with salt responses. We included spatiotemporal expression profiles, expression specificity of each gene, and co-expression and functional gene networks representing 115 transcriptomes sequenced from 35 tissue and developmental stages examining their responses before and after 27 salt treatments in our current study. The highest number of tissue-preferentially expressed genes were found in seeds and siliques while genes in seedlings showed the broadest expression profiles among developmental stages. Seedlings had the highest magnitude of overall transcriptomic responses to salinity compared to mature tissues and developmental stages. Differentially expressed genes in response to salt were largely mutually exclusive but shared common stress response pathways spanning across tissues and developmental stages. Our foundational dataset created for S. parvula representing a stress-adapted wild plant lays the groundwork for future functional, comparative, and evolutionary studies using extremophytes aiming to uncover novel stress tolerant mechanisms. 

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