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1. Lidar survey of ancient Maya settlement in the Puuc region of Yucatan, Mexico

   https://doi.org/https://doi.org/10.1371/journal.pone.0249314  

   Ringle, W. ; Gallareta Negrón, T. ; May Ciau, R. ; Seligson, K. ; Fernandez-Diaz, J. ; Ortegón Zapata, D. ( April 2021 , PloS one)

   Zerboni, A (Ed.)

   The application of lidar remote-sensing technology has revolutionized the practice of settlement and landscape archaeology, perhaps nowhere more so than in the Maya lowlands. This contribution presents a substantial lidar dataset from the Puuc region of Yucatan, Mexico, a cultural subregion of the ancient Maya and a distinct physiographic zone within the Yucatan peninsula. Despite the high density of known sites, no large site has been fully surveyed, and little is known about intersite demography. Lidar technology allows determination of settlement distribution for the first time, showing that population was elevated but nucleated, although without any evidence of defensive features. Population estimates suggest a region among the most densely settled within the Maya lowlands, though hinterland levels are modest. Lacking natural bodies of surface water, the ancient Puuc inhabitants relied upon various storage technologies, primarily chultuns (cisterns) and aguadas (natural or modified reservoirs for potable water). Both are visible in the lidar imagery, allowing calculation of aguada capacities by means of GIS software. The imagery also demonstrates an intensive and widespread stone working industry. Ovens visible in the imagery were probably used for the production of lime, used for construction purposes and perhaps also as a softening agent for maize.more »Quarries can also be discerned, including in some cases substantial portions of entire hills. With respect to agriculture, terrain classification permits identification of patches of prime cultivable land and calculation of their extents. Lidar imagery also provides the first unequivocal evidence for terracing in the Puuc, indeed in all northern Yucatan. Finally, several types of civic architecture and architectural complexes are visible, including four large acropolises probably dating to the Middle Formative period (700–450 B. C.). Later instances of civic architecture include numerous Early Puuc Civic Complexes, suggesting a common form of civic organization at the beginning of the Late Classic demographic surge, (A.D. 600–750).« less
2. Pre-Columbian fire management and control of climate-driven floodwaters over 3,500 years in southwestern Amazonia

   https://doi.org/10.1073/pnas.2022206118  

   Duncan, Neil A. ; Loughlin, Nicholas J. D. ; Walker, John H. ; Hocking, Emma P. ; Whitney, Bronwen S. ( June 2021 , Proceedings of the National Academy of Sciences)

   In landscapes that support economic and cultural activities, human communities actively manage environments and environmental change at a variety of spatial scales that complicate the effects of continental-scale climate. Here, we demonstrate how hydrological conditions were modified by humans against the backdrop of Holocene climate change in southwestern Amazonia. Paleoecological investigations (phytoliths, charcoal, pollen, diatoms) of two sediment cores extracted from within the same permanent wetland, ∼22 km apart, show a 1,500-y difference in when the intensification of land use and management occurred, including raised field agriculture, fire regime, and agroforestry. Although rising precipitation is well known during the mid to late Holocene, human actions manipulated climate-driven hydrological changes on the landscape, revealing differing histories of human landscape domestication. Environmental factors are unable to account for local differences without the mediation of human communities that transformed the region to its current savanna/forest/wetland mosaic beginning at least 3,500 y ago. Regional environmental variables did not drive the choices made by farmers and fishers, who shaped these local contexts to better manage resource extraction. The savannas we observe today were created in the post-European period, where their fire regime and structural diversity were shaped by cattle ranching.
3. Florida mangrove saltmarsh reference surface soils

   https://doi.org/10.6073/pasta/0e08cbe07c84488cb7b9dd16669946d0  

   Lewis, David Bruce ( January 2021 )

   Abstract

   Site description. This data package consists of data obtained from sampling surface soil (the 0-7.6 cm depth profile) in black mangrove (Avicennia germinans) dominated forest and black needlerush (Juncus roemerianus) saltmarsh along the Gulf of Mexico coastline in peninsular west-central Florida, USA. This location has a subtropical climate with mean daily temperatures ranging from 15.4 °C in January to 27.8 °C in August, and annual precipitation of 1336 mm. Precipitation falls as rain primarily between June and September. Tides are semi-diurnal, with 0.57 m median amplitudes during the year preceding sampling (U.S. NOAA National Ocean Service, Clearwater Beach, Florida, station 8726724). Sea-level rise is 4.0 ± 0.6 mm per year (1973-2020 trend, mean ± 95 % confidence interval, NOAA NOS Clearwater Beach station). The A. germinans mangrove zone is either adjacent to water or fringed on the seaward side by a narrow band of red mangrove (Rhizophora mangle). A near-monoculture of J. roemerianus is often adjacent to and immediately landward of the A. germinans zone. The transition from the mangrove to the J. roemerianus zone is variable in our study area. An abrupt edge between closed-canopy mangrove and J. roemerianus monoculture may extend for up to several hundred meters in some locations, while other stretches of ecotone present a gradual transition where smaller, widely spaced trees are interspersed into the herbaceous marsh. Juncus roemerianus then extends landward to a high marsh patchwork of succulent halophytes (including Salicornia bigellovi, Sesuvium sp., and Batis maritima), scattered dwarf mangrove, and salt pans, followed in turn by upland vegetation that includes Pinus sp. and Serenoa repens. Field design and sample collection. We established three study sites spaced at approximately 5 km intervals along the western coastline of the central Florida peninsula. The sites consisted of the Salt Springs (28.3298°, -82.7274°), Energy Marine Center (28.2903°, -82.7278°), and Green Key (28.2530°, -82.7496°) sites on the Gulf of Mexico coastline in Pasco County, Florida, USA. At each site, we established three plot pairs, each consisting of one saltmarsh plot and one mangrove plot. Plots were 50 m^2 in size. Plots pairs within a site were separated by 230-1070 m, and the mangrove and saltmarsh plots composing a pair were 70-170 m apart. All plot pairs consisted of directly adjacent patches of mangrove forest and J. roemerianus saltmarsh, with the mangrove forests exhibiting a closed canopy and a tree architecture (height 4-6 m, crown width 1.5-3 m). Mangrove plots were located at approximately the midpoint between the seaward edge (water-mangrove interface) and landward edge (mangrove-marsh interface) of the mangrove zone. Saltmarsh plots were located 20-25 m away from any mangrove trees and into the J. roemerianus zone (i.e., landward from the mangrove-marsh interface). Plot pairs were coarsely similar in geomorphic setting, as all were located on the Gulf of Mexico coastline, rather than within major sheltering formations like Tampa Bay, and all plot pairs fit the tide-dominated domain of the Woodroffe classification (Woodroffe, 2002, "Coasts: Form, Process and Evolution", Cambridge University Press), given their conspicuous semi-diurnal tides. There was nevertheless some geomorphic variation, as some plot pairs were directly open to the Gulf of Mexico while others sat behind keys and spits or along small tidal creeks. Our use of a plot-pair approach is intended to control for this geomorphic variation. Plot center elevations (cm above mean sea level, NAVD 88) were estimated by overlaying the plot locations determined with a global positioning system (Garmin GPS 60, Olathe, KS, USA) on a LiDAR-derived bare-earth digital elevation model (Dewberry, Inc., 2019). The digital elevation model had a vertical accuracy of ± 10 cm (95 % CI) and a horizontal accuracy of ± 116 cm (95 % CI). Soil samples were collected via coring at low tide in June 2011. From each plot, we collected a composite soil sample consisting of three discrete 5.1 cm diameter soil cores taken at equidistant points to 7.6 cm depth. Cores were taken by tapping a sleeve into the soil until its top was flush with the soil surface, sliding a hand under the core, and lifting it up. Cores were then capped and transferred on ice to our laboratory at the University of South Florida (Tampa, Florida, USA), where they were combined in plastic zipper bags, and homogenized by hand into plot-level composite samples on the day they were collected. A damp soil subsample was immediately taken from each composite sample to initiate 1 y incubations for determination of active C and N (see below). The remainder of each composite sample was then placed in a drying oven (60 °C) for 1 week with frequent mixing of the soil to prevent aggregation and liberate water. Organic wetland soils are sometimes dried at 70 °C, however high drying temperatures can volatilize non-water liquids and oxidize and decompose organic matter, so 50 °C is also a common drying temperature for organic soils (Gardner 1986, "Methods of Soil Analysis: Part 1", Soil Science Society of America); we accordingly chose 60 °C as a compromise between sufficient water removal and avoidance of non-water mass loss. Bulk density was determined as soil dry mass per core volume (adding back the dry mass equivalent of the damp subsample removed prior to drying). Dried subsamples were obtained for determination of soil organic matter (SOM), mineral texture composition, and extractable and total carbon (C) and nitrogen (N) within the following week. Sample analyses. A dried subsample was apportioned from each composite sample to determine SOM as mass loss on ignition at 550 °C for 4 h. After organic matter was removed from soil via ignition, mineral particle size composition was determined using a combination of wet sieving and density separation in 49 mM (3 %) sodium hexametaphosphate ((NaPO_3)_6) following procedures in Kettler et al. (2001, Soil Science Society of America Journal 65, 849-852). The percentage of dry soil mass composed of silt and clay particles (hereafter, fines) was calculated as the mass lost from dispersed mineral soil after sieving (0.053 mm mesh sieve). Fines could have been slightly underestimated if any clay particles were burned off during the preceding ignition of soil. An additional subsample was taken from each composite sample to determine extractable N and organic C concentrations via 0.5 M potassium sulfate (K_2SO_4) extractions. We combined soil and extractant (ratio of 1 g dry soil:5 mL extractant) in plastic bottles, reciprocally shook the slurry for 1 h at 120 rpm, and then gravity filtered it through Fisher G6 (1.6 μm pore size) glass fiber filters, followed by colorimetric detection of nitrite (NO_2^-) + nitrate (NO_3^-) and ammonium (NH_4^+) in the filtrate (Hood Nowotny et al., 2010,Soil Science Society of America Journal 74, 1018-1027) using a microplate spectrophotometer (Biotek Epoch, Winooski, VT, USA). Filtrate was also analyzed for dissolved organic C (referred to hereafter as extractable organic C) and total dissolved N via combustion and oxidation followed by detection of the evolved CO_2 and N oxide gases on a Formacs HT TOC/TN analyzer (Skalar, Breda, The Netherlands). Extractable organic N was then computed as total dissolved N in filtrate minus extractable mineral N (itself the sum of extractable NH_4-N and NO_2-N + NO_3-N). We determined soil total C and N from dried, milled subsamples subjected to elemental analysis (ECS 4010, Costech, Inc., Valencia, CA, USA) at the University of South Florida Stable Isotope Laboratory. Median concentration of inorganic C in unvegetated surface soil at our sites is 0.5 % of soil mass (Anderson, 2019, Univ. of South Florida M.S. thesis via methods in Wang et al., 2011, Environmental Monitoring and Assessment 174, 241-257). Inorganic C concentrations are likely even lower in our samples from under vegetation, where organic matter would dilute the contribution of inorganic C to soil mass. Nevertheless, the presence of a small inorganic C pool in our soils may be counted in the total C values we report. Extractable organic C is necessarily of organic C origin given the method (sparging with HCl) used in detection. Active C and N represent the fractions of organic C and N that are mineralizable by soil microorganisms under aerobic conditions in long-term soil incubations. To quantify active C and N, 60 g of field-moist soil were apportioned from each composite sample, placed in a filtration apparatus, and incubated in the dark at 25 °C and field capacity moisture for 365 d (as in Lewis et al., 2014, Ecosphere 5, art59). Moisture levels were maintained by frequently weighing incubated soil and wetting them up to target mass. Daily CO_2 flux was quantified on 29 occasions at 0.5-3 week intervals during the incubation period (with shorter intervals earlier in the incubation), and these per day flux rates were integrated over the 365 d period to compute an estimate of active C. Observations of per day flux were made by sealing samples overnight in airtight chambers fitted with septa and quantifying headspace CO_2 accumulation by injecting headspace samples (obtained through the septa via needle and syringe) into an infrared gas analyzer (PP Systems EGM 4, Amesbury, MA, USA). To estimate active N, each incubated sample was leached with a C and N free, 35 psu solution containing micronutrients (Nadelhoffer, 1990, Soil Science Society of America Journal 54, 411-415) on 19 occasions at increasing 1-6 week intervals during the 365 d incubation, and then extracted in 0.5 M K_2SO_4 at the end of the incubation in order to remove any residual mineral N. Active N was then quantified as the total mass of mineral N leached and extracted. Mineral N in leached and extracted solutions was detected as NH_4-N and NO_2-N + NO_3-N via colorimetry as above. This incubation technique precludes new C and N inputs and persistently leaches mineral N, forcing microorganisms to meet demand by mineralizing existing pools, and thereby directly assays the potential activity of soil organic C and N pools present at the time of soil sampling. Because this analysis commences with disrupting soil physical structure, it is biased toward higher estimates of active fractions. Calculations. Non-mobile C and N fractions were computed as total C and N concentrations minus the extractable and active fractions of each element. This data package reports surface-soil constituents (moisture, fines, SOM, and C and N pools and fractions) in both gravimetric units (mass constituent / mass soil) and areal units (mass constituent / soil surface area integrated through 7.6 cm soil depth, the depth of sampling). Areal concentrations were computed as X × D × 7.6, where X is the gravimetric concentration of a soil constituent, D is soil bulk density (g dry soil / cm^3), and 7.6 is the sampling depth in cm.
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4. Ancient DNA and deep population structure in sub-Saharan African foragers

   https://doi.org/10.1038/s41586-022-04430-9  

   Lipson, Mark ; Sawchuk, Elizabeth A. ; Thompson, Jessica C. ; Oppenheimer, Jonas ; Tryon, Christian A. ; Ranhorn, Kathryn L. ; de Luna, Kathryn M. ; Sirak, Kendra A. ; Olalde, Iñigo ; Ambrose, Stanley H. ; et al ( March 2022 , Nature)

   Abstract Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa 1–4 . Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations 3,5 . Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalizationmore »at the end of the Pleistocene epoch.« less
5. Response of Green Lake, Wisconsin, to Changes in Phosphorus Loading, With Special Emphasis on Near-Surface Total Phosphorus Concentrations and Metalimnetic Dissolved Oxygen Minima

   https://doi.org/10.3133/sir20225003  

   Robertson, D.M. ( January 2022 , Scientific investigations report)

   Green Lake is the deepest natural inland lake in Wisconsin, with a maximum depth of about 72 meters. In the early 1900s, the lake was believed to have very good water quality (low nutrient concentrations and good water clarity) with low dissolved oxygen (DO) concentrations occurring in only the deepest part of the lake. Because of increased phosphorus (P) inputs from anthropogenic activities in its watershed, total phosphorus (TP) concentrations in the lake have increased; these changes have led to increased algal production and low DO concentrations not only in the deepest areas but also in the middle of the water column (metalimnion). The U.S. Geological Survey has routinely monitored the lake since 2004 and its tributaries since 1988. Results from this monitoring led the Wisconsin Department of Natural Resources (WDNR) to list the lake as impaired because of low DO concentrations in the metalimnion, and they identified elevated TP concentrations as the cause of impairment. As part of this study by the U.S. Geological Survey, in cooperation with the Green Lake Sanitary District, the lake and its tributaries were comprehensively sampled in 2017–18 to augment ongoing monitoring that would further describe the low DO concentrations in the lake (especiallymore »in the metalimnion). Empirical and process-driven water-quality models were then used to determine the causes of the low DO concentrations and the magnitudes of P-load reductions needed to improve the water quality of the lake enough to meet multiple water-quality goals, including the WDNR’s criteria for TP and DO. Data from previous studies showed that DO concentrations in the metalimnion decreased slightly as summer progressed in the early 1900s but, since the late 1970s, have typically dropped below 5 milligrams per liter (mg/L), which is the WDNR criterion for impairment. During 2014–18 (the baseline period for this study), the near-surface geometric mean TP concentration during June–September in the east side of the lake was 0.020 mg/L and in the west side was 0.016 mg/L (both were above the 0.015-mg/L WDNR criterion for the lake), and the metalimnetic DO minimum concentrations (MOMs) measured in August ranged from 1.0 to 4.7 mg/L. The degradation in water quality was assumed to have been caused by excessive P inputs to the lake; therefore, the TP inputs to the lake were estimated. The mean annual external P load during 2014–18 was estimated to be 8,980 kilograms per year (kg/yr), of which monitored and unmonitored tributary inputs contributed 84 percent, atmospheric inputs contributed 8 percent, waterfowl contributed 7 percent, and septic systems contributed 1 percent. During fall turnover, internal sediment recycling contributed an additional 7,040 kilograms that increased TP concentrations in shallow areas of the lake by about 0.020 mg/L. The elevated TP concentrations then persisted until the following spring. On an annual basis, however, there was a net deposition of P to the bottom sediments. Empirical models were used to describe how the near-surface water quality of Green Lake would be expected to respond to changes in external P loading. Predictions from the models showed a relatively linear response between P loading and TP and chlorophyll-a (Chl-a) concentrations in the lake, with the changes in TP and Chl-a concentrations being less on a percentage basis (50–60 percent for TP and 30–70 percent for Chl-a) than the changes in P loading. Mean summer water clarity, quantified by Secchi disk depths, had a greater response to decreases in P loading than to increases in P loading. Based on these relations, external P loading to the lake would need to be decreased from 8,980 kg/yr to about 5,460 kg/yr for the geometric mean June–September TP concentration in the east side of the lake, with higher TP concentrations than in the west side, to reach the WDNR criterion of 0.015 mg/L. This reduction of 3,520 kg/yr is equivalent to a 46-percent reduction in the potentially controllable external P sources (all external sources except for precipitation, atmospheric deposition, and waterfowl) from those measured during water years 2014–18. The total external P loading would need to decrease to 7,680 kg/yr (a 17-percent reduction in potentially controllable external P sources) for near-surface June–September TP concentrations in the west side of the lake to reach 0.015 mg/L. Total external P loading would need to decrease to 3,870–5,320 kg/yr for the lake to be classified as oligotrophic, with a near-surface June–September TP concentration of 0.012 mg/L. Results from the hydrodynamic water-quality model GLM–AED (General Lake Model coupled to the Aquatic Ecodynamics modeling library) indicated that MOMs are driven by external P loading and internal sediment recycling that lead to high TP concentrations during spring and early summer, which in turn lead to high phytoplankton production, high metabolism and respiration, and ultimately DO consumption in the upper, warmer areas of the metalimnion. GLM–AED results indicated that settling of organic material during summer might be slowed by the colder, denser, and more viscous water in the metalimnion and thus increase DO consumption. Based on empirical evidence from a comparison of MOMs with various meteorological, hydrologic, water quality, and in-lake physical factors, MOMs were lower during summers, when metalimnetic water temperatures were warmer, near-surface Chl-a and TP concentrations were higher, and Secchi depths were lower. GLM–AED results indicated that the external P load would need to be reduced to about 4,060 kg/yr, a 57-percent reduction from that measured in 2014–18, to eliminate the occurrence of MOMs less than 5 mg/L during more than 75 percent of the years (the target provided by the WDNR). Large reductions in external P loading are expected to have an immediate effect on the near-surface TP concentrations and metalimnetic DO concentrations in Green Lake; however, it may take several years for the full effects of the external-load reduction to be observed because internal sediment recycling is an important source of P for the following spring.« less