Modern Samples Research Articles

Late-Holocene environmental conditions revealed by a small mammal assemblage in mountain areas of Northwestern Argentina

Based on a diverse Late-Holocene (1889–1743 cal yrs BP) small mammal assemblage (14 species, 204 individuals) resulting from the trophic activity of owls, we reconstruct the paleoenvironmental conditions of Las Chacritas area, Catamarca Province, northwestern Argentina. Twenty modern and one additional Late-Holocene samples from the region were used as comparative parameters in the paleoenvironmental reconstruction. Through direct comparison with a present-day assemblage from Las Chacritas, and using Nonmetric Multidimensional Scaling, spatial and temporal beta diversity (employing the Sorensen dissimilarity index), and the temporal beta diversity index (TBI) including all the small mammal samples, we quantitatively reconstruct the relationships among modern and Late-Holocene assemblages. Direct comparison showed significant differences, with relative abundances changing markedly over time, with several species of the Late-Holocene assemblage absent in the modern sample whereas many species frequent in the modern community absent in the Late-Holocene. NMDS analysis associated the Late-Holocene assemblage with modern samples of western drier environments. Beta diversity was low for presence-absence and moderate for abundance data, with higher contribution of turnover than nestedness, although for abundance data the proportion of nestedness was higher. TBI showed high variation among both Holocene sites and their present-day counterparts, whereas species gains dominated in modern samples. Our results suggest that the habitats surrounding Las Chacritas have modified markedly since the Late-Holocene. Presence of species today frequent in arid environments and absence of forest-dwelling species suggest that open, dry and relatively rocky habitats characterized this area in that interval.

Distribution of 3-hydroxy fatty acids in South China Sea since the last deglaciation: Applicability of 3-hydroxy fatty acid-based palaeothermometry

3-Hydroxy fatty acids (3-OH-FAs) are biomarkers for Gram-negative bacteria. Recent research has suggested that they could serve as temperature proxies in both terrestrial and marine environments, based on calibrations using modern samples. However, these proxies have been only applied in a speleothem for the Holocene and a short sediment core in the East China Sea for past 58 years, thus more evidence is needed to testify their validity. In this study, we analyzed the distribution of 3-OH-FAs in a sediment core from the northern South China Sea (SCS) spanning the past 19 thousand years (19 ka). We detected 3-OH-FAs, including normal (n-), iso (i-), and anteiso (a-) isomers, in all 56 samples with carbon numbers ranging from 10 to 18. The distribution of 3-OH-FAs in marine sediments differed from that in terrestrial sediments (soil, stalagmite, and lake sediments), with a higher fractional abundance of anteiso-FAs. Two temperature proxies, RANs and RAN13, showed a positive correlation (R2 = 0.5; p < 0.001), with RANs-SST being closer to the actual sea surface temperature (SST). The reconstructed RANs-SST in our core exhibited a typical glacial-Holocene increase of 2–3 °C (20.8 ± 2.7 °C vs. 24.1 ± 1.3 °C). Several abrupt climate events, such as the Younger Dryas, BØlling/AllerØd, and Heinrich Event 1, were also recorded in RANs-SST. Therefore, our study supports the applicability of 3-OH-FA RANs as a temperature proxy for paleoenvironmental reconstructions, at least in the last glacial periods.

Source apportionment of suspended particulate organic matter in a shallow eutrophic lake of Southwest China using MixSIAR model

Eutrophication has become prominent in many lakes of the world, resulting in a continuous rise of suspended particulate organic matter (POM) that can be of vital consequence for water quality and carbon cycling. While the accumulation and decomposition of POM can enhance nutrient cycling at a rate depending on the property of lake-water organic carbon, it is important to identify the source of suspended POM for evaluating eutrophication and carbon burial. Here we analyzed the distribution of stable isotopic ratios (δ13C and δ15N) and the carbon/nitrogen ratio (C/N) in suspended POM in a shallow eutrophic lake of subtropical China, for apportioning the POM sources using Bayesian mixing model. Specifically, we collected seasonal samples of lake-water POM (>0.7 μm) from 20 sites in Yilong Lake from September 2020 to June 2022, as well as six types of modern samples covering the main carbon sources in the catchment. The spatial surveys showed that in the dry year (low water level) the δ13C of POM was more enriched in the western basin than those in the central and eastern basins, while the seasonal surveys showed the most enriched δ13C of POM in September. However, this spatio-temporal heterogeneity disappeared in the wet year (high water level). It was also found that the δ13C, δ15N and C/N values of POM varied significantly with those of phytoplankton across sites and seasons. Application of the MixSIAR model further showed that phytoplankton was the predominant source of POM in Yilong Lake (79.8 ± 13.4 %), but with large annual difference, 68.9 ± 10.3 % in the dry year and 90.7 ± 3.7 % in the wet year. In comparison, the contribution of the other five endmembers was much more moderate. In particular, the proportion of allochthonous organic carbon in POM was relatively low, with terrestrial plants and soils contributing 6.1 ± 4.8 % and 4.3 ± 2.5 % of POM, respectively. Our quantitative evidence for the dominance of the autochthonous source (i.e., phytoplankton) in lake-water POM over time and space suggested a determining role of eutrophication in the composition of lake organic carbon. Therefore, the coupling of algal blooms with organic carbon cycling in inland waters can be enhanced with continuous catchment development and regional warming.

Skeletal manifestations of anemia in the sternum in a modern clinical sample: An initial investigation

Anemia is a globally significant condition, both today and throughout history. Studying how it affected past communities contributes to understanding its impact on vulnerable groups. However, anemia diagnosis in skeletal remains is challenging, and improving methods for diagnosis is necessary for moving forward. In current clinical practice, sternal bone marrow undergoes anemia-related changes, which could affect underlying bone structure, but the sternum has never been investigated as a skeletal marker of anemia. We used a cohort of individuals with known hematological data (N = 23) to investigate whether there are quantitative bone changes in the sternum of individuals clinically diagnosed with anemia. Sternal bone features were measured using CT imaging to calculate a ratio of the relative cortical bone to trabecular space sample. The sample was separated into non-anemic and anemic cohorts based on World Health Organization diagnostic parameters. We found significant differences in ratios between those with and without anemia, suggesting that sternal bone ratio measurements could be used as a diagnostic parameter. In individuals without clinically-diagnosed anemia, ratios never exceeded 3.6 in the manubrium and 2.3 in the sternal body. We repeated these ratio measurements using micro-CT analysis on a sample of archaeological sternums and found that the ratio diagnostic parameter could also be used in this sample to identify those who could have experienced anemia. These results demonstrate the utility of quantitative methods for diagnosing anemia in skeletal remains and suggest that sternal ratio measurements can be used as part of anemia diagnosis in past contexts.

Assessing the diet of modern and archaeological guanacos from the Great Chaco in Córdoba, Argentina, through stable isotope analysis (δ13C, δ15N) of bone and dentin collagen: Implications for paleoenvironmental and zooarchaeological studies

The application of stable isotope analyses allows a diachronic characterisation of species habitat and feeding behaviour, information of utmost importance for zooarchaeological research. In South America, the former distribution of the guanaco ( Lama guanicoe) encompassed a much larger territory than the current one. Within the Argentinean Great Chaco, only a small native population persists in Northwestern Córdoba province, Central Argentina, where it was once widely distributed. In this paper, we present the first set of dentin and collagen δ13C and δ15N values for this relict population ( N = 18) along with archaeological data of guanaco specimens ( N = 19) dated to the Middle and Late Holocene from the nearby Ongamira valley. Neither deciduous and permanent teeth nor males and females show marked differences within the modern samples. Both modern and archaeological guanaco δ13C values indicate a mixed diet of C3 and, to a lesser extent, C4 plants. Conversely, the δ15N values exhibit distinct signals between the Arid and the Mountain Chaco subregions. The diet breadth of the archaeological guanacos suggests the use of transitional or ecotonal environments, also reflected in the size of their isotopic niche as opposed to modern guanacos. Regarding the timing of the species retraction in the region, there is no evidence of a shift in its habitat during the period between ~4700 and 190014C years BP. We suggest their retraction probably occurred later than previously proposed in regional zooarchaeological models.

Dietary change of North Patagonian guanacos: A historical ecology perspective through the study of stable isotopes

This paper presents the results of a study on the isotopic ecology of guanacos in central western Argentina. We examine the historical population ecology of guanacos using stable isotope analysis of bone collagen from pre-Hispanic and modern guanaco populations ( n = 129), considering variability in two ecoregions: the Monte hot desert and the Andean-Patagonian cold desert. Our study addresses the consistency of guanaco diets over time, evaluating palaeoecology to provide information for conservation of this taxon. We found significant differences in isotopic niche size between modern and archaeological guanacos. When analyzed by ecoregion, there were significant differences in niche size through time, indicating that guanacos had distinctive dietary habits and occupied different ecological niches across the ecoregions. Comparing Standard Ellipse Areas (SEA) through time and across space, we observed that the archaeological SEA for guanacos is smaller than its modern counterpart in the Andean-Patagonia ecoregion. Conversely, in Monte, the archaeological SEA is larger than the one established for modern samples. The contrast between pre-Hispanic and modern populations highlight the impact of human activity and conservation efforts on the distribution and ecology of guanacos. These findings have important implications for understanding guanaco ecology with consequences for conservation policies.

Insular evolution from an archaeological perspective: a case study of Orkney house mouse

Abstract Archaeological material adds a temporal dimension to evolutionary studies that is valuable for elucidating long-term population stability and evolutionary shifts for species closely associated with humans. Here, a two-dimensional geometric morphometrics approach on first upper molars was applied to modern and archaeological samples to assess the evolution of house mice in Orkney, an archipelago north of Scotland. Modern populations included localities in Orkney, north Scotland, and France. Two archaeological sites in Orkney represented the Norse period: Birsay Beachview (Mainland) and Tuquoy (Westray) (10th–14th/15th centuries AD). The archaeological specimens were larger than modern specimens from similar settings, suggesting processes leading to a recent decline in the size of Orkney house mice. Molar morphology and associated non-metric traits distinct to the Orkney lineage were already established in the Norse period, as indicated by morphological similarity of the Birsay samples to modern Orkney and north Scotland populations. Stability of human settlement is likely to influence morphological evolution in house mice. The Birsay site, located in Birsay village, which has been inhabited since Norse times, might represent the ancestral house mouse population in Orkney. Tuquoy, a settlement abandoned by the end of the medieval period, provided samples different from modern house mouse populations in Westray and neighbouring isles.

Successive Protein Extraction Using Hydroxylamine to Increase the Depth of Proteome Coverage in Fresh, Forensic, and Archaeological Bones.

Proteomics is continually being applied to a wider range of applications, now including the analysis of archaeological samples and anatomical specimens, particularly collagen-containing tissues such as bones and teeth. Here, we present the application of a chemical digestion-based proteomics sample preparation protocol to the analysis of fresh, anatomical, and archaeological samples. We describe and discuss two protocols: one that uses hydroxylamine as an additional step of the proteomic workflow, applied to the insoluble fraction, and another that applies hydroxylamine directly on demineralized bones and teeth. We demonstrate the additional information that can be extracted using both protocols, including an increase in the sequence coverage and number of peptides detected in modern and archaeological samples and an increase in the number of proteins identified in archaeological samples. By targeting research related to collagens or extracellular matrix proteins, the use of this protocol will open new insights, considering both fresh and ancient mineralized samples.

RADIOCARBON AND URANIUM PROFILES IN MARINE GASTROPODS AROUND THE JAPANESE ARCHIPELAGO

ABSTRACT In this study, we investigate the distribution of radiocarbon and uranium in the calcified opercula of Turbo sp. collected from Ryukyu region and Chiba, Japan, to explore the potential of U/Th dating using mollusks collected from the Japanese archipelago. We acquired high-resolution radiocarbon and uranium concentration measurements using single-stage accelerator mass spectrometry and laser ablation−inductively coupled plasma−mass spectrometry. Our results show that uranium in the opercula of modern Turbo sp. is unevenly distributed at concentrations 1000 times less than those in coral skeletons. Radiocarbon found in the calcified opercula samples record ambient seawater radiocarbon values as well as coral skeletons. Uranium in the calcified opercula of Holocene Turbo marmoratus were also unevenly distributed and concentrated within the opercula in a different manner than observed in modern samples, suggesting uranium exchange after death. Our results suggest variable uptake of uranium isotopes into mollusk shells and highlights the need for rigorous sample selection criteria when choosing mollusks species for U/Th dating around Japan.

Wide-spread dispersal in a deep-sea brooding polychaete: the role of natural history collections in assessing the distribution in quill worms (Onuphidae, Annelida)

BackgroundModern integrative taxonomy-based annelid species descriptions are detailed combining morphological data and, since the last decades, also molecular information. Historic species descriptions are often comparatively brief lacking such detail. Adoptions of species names from western literature in the past led to the assumption of cosmopolitan ranges for many species, which, in many cases, were later found to include cryptic or pseudocryptic lineages with subtle morphological differences. Natural history collections and databases can aid in assessing the geographic ranges of species but depend on correct species identification. Obtaining DNA sequence information from wet-collection museum specimens of marine annelids is often impeded by the use of formaldehyde and/or long-term storage in ethanol resulting in DNA degradation and cross-linking.ResultsThe application of ancient DNA extraction methodology in combination with single-stranded DNA library preparation and target gene capture resulted in successful sequencing of a 110-year-old collection specimen of quill worms. Furthermore, a 40-year-old specimen of quill worms was successfully sequenced using a standard extraction protocol for modern samples, PCR and Sanger sequencing. Our study presents the first molecular analysis of Hyalinoecia species including the previously known species Hyalinoecia robusta, H. tubicloa, H. artifex, and H. longibranchiata, and a potentially undescribed species from equatorial western Africa morphologically indistinguishable from H. tubicola. The study also investigates the distribution of these five Hyalinoecia species. Reassessing the distribution of H. robusta reveals a geographical range covering both the Atlantic and the Indian Oceans as indicated by molecular data obtained from recent and historical specimens.ConclusionOur results represent an example of a very wide geographical distribution of a brooding deep-sea annelid with a complex reproduction strategy and seemingly very limited dispersal capacity of its offspring, and highlights the importance of molecular information from museum specimens for integrative annelid taxonomy and biogeography.

Proteomic Analysis of Collagen: a Mass Spectrometry Approach to Material Identification of Shadow Puppet Cultural Relics.

Shadow puppets are a popular art form in various regions, including China, Indonesia, and Turkey, and are rich in cultural significance. However, there is a considerable lack of research on the materials, diseases and conservation techniques related to shadow puppet relics. Material identification is the basis for understanding the production process of ancient shadow puppet relics and evaluating their deterioration degree. The microscopic morphology and infrared spectroscopy results in our experiments showed that the traditional methods of ancient skin identification were not effective in the shadow puppet samples. In order to achieve accurate identification, we used biological mass-spectrometry in proteomics to examine two puppet relics and commercially available modern shadow puppets. The results showed that the above samples could be detected by mass spectrometry with abundant peptides, including peptides specific for bovine skin. These peptides cannot be found in other commonly used materials for making shadow puppets, including the skins of pig, sheep, deer and horse. It is worth mentioning that we have found the peptides specific to yellow cowhide in two ancient shadow puppet relics samples. Therefore, the proteomic evidence shows that the raw materials of the two shadow puppet relics samples are yellow cowhide. Four modern samples also confirmed the reliability of material identification using proteomics. The proteomic evidence shows that the biological mass spectrometry will contribute to the scientific research of shadow puppet relics and other skin and leather cultural relics.

Preservation of bone organic fraction is not predictive of the preservation of bone inorganic fraction when assessing stable isotope analysis sample quality control measures

Stable isotope analysis of carbon (C), nitrogen (N), hydrogen (H), and oxygen (O) of archaeological bone has become an increasingly common research method for interpreting human behavior in the past. However, diagenesis of skeletal material can invalidate stable isotope ratios, thereby compromising interpretations. We examine patterns of bone diagenesis using infrared spectroscopy of bone bioapatite samples in relation to indicators of organic preservation quality indicators. We assess crystallinity, an indicator of bioapatite preservation, using the infrared splitting factor (IR-SF) and carbonate content (carbonate to phosphate ratio, C/P) calculated from infrared spectra. We then test the assumption that if the organic fraction of bone is preserved, the mineral fraction will also be unaffected by postmortem chemical alteration. We analyzed 454 bone bioapatite and extracted bone organic sample pairs from modern, historic, and prehistoric humans. Consistent with previous studies, we observed a strong, statistically significant negative linear relationship between IR-SF and C/P (r = −0.855, p < 0.001). Modern bone bioapatite samples unaltered by diagenesis have low IR-SF and high C/P values. There was no significant association between the collagen yield or atomic C:N ratio and IR-SF or C/P values. The range of variation in IR-SF and C/P values for samples with organic yields between 0 and >20 percent spanned the range of modern bone bioapatite unaltered by diagenesis as well as bone bioapatite significantly affected by diagenesis. The lack of predictive patterning between bone inorganic and organic diagenesis suggests that the depositional context and site formation history play critical and independent roles in the organic and mineral fraction of bone. Thus, the preservation of the organic fraction of bone is not predictive of the preservation of the inorganic fraction (e.g., bioapatite).

REACTIVE FLOW IN CARBONATE ROCKS FROM LACUSTRINE ENVIRONMENTS: THE EFFECTS OF PRESSURE AND FLUID SALINITY

The high production of CO2 from Brazilian pre-salt reservoirs requires research on CO2 interactions with carbonate reservoirs for enhanced oil recovery (EOR) or CO2 trapping. This interaction causes reactive phenomena that are not fully understood. Experimental tests on carbonate facies are crucial for understanding reactions and their impact on reservoir characteristics. This study investigates experimentally reactions generated by reactive fluid flow in carbonate rocks from two geological scenarios by analyzing chemical and morphological parameters before and after the tests. Salinity was the most significant parameter for reactive flow, impacting porosity for modern continental carbonate samples from Patagonia. However, the sample from the Brazilian pre-salt showed higher mineral stability and less mineral dissolution. Results provide data for simulating reactive transport in these rocks for CCS and understanding diagenetic processes' impact on reservoir quality.

Study on Antimicrobial Activity of Chromolaena odorata and Aerva lanata

Purpose: Numerous natural products from traditional medicinal plants have extensive chances for new steers to drug development because of the obtainability of chemical diverseness. Advanced modern methods are developed for the extraction, which are pointed to be the critical move in formulation of plants. These latest approaches of extraction are more effectual than the antient extraction methods for the effective development of traditional herbal remedies. For the greater extraction and study of medicinal plants, scientists prefer modern sample- preparation techniques over conventional techniques as they ensure the better-quality herbal products to the worldwide consumers. The interest in plant based therapeutic drugs and comestible plants has grown all over the World, since the increase in stipulation for chemical diverseness in investigation programs. Design/Methodology/Approach: The study examines how different plant extract concentrations and extraction solvents affect the antimicrobial activity of several therapeutic plants. The traditional mechanical method is used for extraction. Chromolaena odorata and Aerva lanata were the medicinal plants chosen for the extraction. Different concentrations of the extracts were made such as 1%, 10% and 50%. Diethyl ether, sterile distilled water and ethanol are the solvents used for extraction. Two common techniques were used to observe whether the selected plants have any antimicrobial activity against the organisms, which were agar disc diffusion and well diffusion method. Klebsiella pneumonia, Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus Staphylococcus aureus were the microorganisms selected for this study. Findings/Result: Among the selected extracts, aqueous extract gave more activity against infectious microbes. C. odorata showed better reaction with S. aureus, K. pneumonia and B. subtilis, were as A. lanata found well reactive against P. aeruginosa, S. aureus and K. pneumonia. Originality/Value: This study gives us an outline about the antimicrobial activity of C. orodata and A. lanata on various infectious microbes, based on the collected data. Paper type: Case study based research approach.

Search for differentially methylated regions in ancient and modern genomes

Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter­gatherer to a sedentary lifestyle. The application of existing whole­genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter­gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15–20 %. Additionally, we developed a new Python­based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two­step data processing approach, where the first step involves the identification and filtration of tissue­specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher’s target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.

Sediment records from Lake Nipissing (ON, Canada) register a lake-wide multi-trophic response to climate change and reveal its possible role for increased cyanobacterial blooms

Recurring cyanobacterial blooms have been reported in Lake Nipissing (Ontario, Canada) since at least 2000. However, monitoring data indicate that surface water nutrient concentrations have not increased over the past ∼45 years in this large, shallow, mesotrophic lake. Applying paleolimnological methods, we establish baseline environmental conditions and extend the Lake Nipissing water quality data to pre-industrial times. Lake-wide assessment of changes in nutrient status, algal production, and effects of climate warming are provided by examining: 1) modern and pre-industrial sedimentary diatom assemblages from nine locations; 2) temporal trends in sedimentary photosynthetic pigments over ∼200 years from five locations; and 3) detailed sedimentary profiles of diatom and chironomid assemblage composition from Callander Bay, spanning the past ∼200 years. A pronounced shift in diatom assemblage composition was registered at all sites with pre-industrial sediments dominated by Aulacoseira spp. and modern samples dominated by Discostella stelligera. The detailed diatom analysis for Callander Bay indicated that this shift occurred ca. 1990. Since ca. 1975, cyanobacterial production (spectrally inferred from sediments) exceeded the ∼200-year mean and matches the observed increase in bloom reports. Twentieth century shifts in chironomid assemblages in Callander Bay from Procladius to Chironomus spp. dominance indicate lower hypolimnetic oxygen in recent decades. Collectively, these changes suggest that previously polymictic Lake Nipissing is now experiencing periods of thermal stratification and development of transient anoxia in bottom waters. These conditions are more prevalent and widespread in modern Lake Nipissing, consistent with a response to recent warming, decreased wind speed, and a longer ice-free period.

Risk-oriented approach in the problems of modeling of metrological support of the measuring instrument fleet

The methods of management of metrological support of the measuring instrument fleet are considered. The modern situation is described, when the fleet of measuring instruments is heterogeneous and includes both obsolete samples of measuring instruments with a long service life and significant operating time, and the newest, high-tech samples of measuring instruments. At the same time the proportions between the mentioned groups of measuring instruments change over time, as the ageing of measuring instruments and their transition from one group to another takes place. Also the measurement instrument park is renewed as a result of purchases of new and modernization of existing samples. The heterogeneity of the measuring instrument park leads to the necessity of development and application of new methods of management of metrological support of the measuring instrument park, including the use of mathematical modeling. One of the promising methods of metrological management of the measuring instrument fleet based on the risk-oriented approach is proposed. The probability of finding a randomly selected sample of measuring instruments from the measurement instrument park at an arbitrary moment of time in the state of unreadiness for intended use is used as a risk indicator for the measuring instrument park. In accordance with the risk-oriented approach the measuring instrument park is divided into risk classes. The algorithm of assigning measuring instruments to different risk classes is developed, based on solving a series of optimization problems of the fleet operation taking into account the processes of aging and renewal of the fleet of measuring instruments. The results of application of the risk-oriented approach in the problem of modeling of metrological support of heterogeneous fleet of measuring instruments including both modern and obsolete samples with different metrological characteristics, MTBF and lifetime are presented. It is shown that by dividing all samples of measuring instruments into risk classes and carrying out verifications with their close to optimal periodicity and with their tolerance for controlled parameters in each risk class it is possible to minimize the total average risk for the fleet of measuring instruments and at the same time to achieve resource saving.

Haplotype-based inference of recent effective population size in modern and ancient DNA samples

Individuals sharing recent ancestors are likely to co-inherit large identical-by-descent (IBD) genomic regions. The distribution of these IBD segments in a population may be used to reconstruct past demographic events such as effective population size variation, but accurate IBD detection is difficult in ancient DNA data and in underrepresented populations with limited reference data. In this work, we introduce an accurate method for inferring effective population size variation during the past ~2000 years in both modern and ancient DNA data, called HapNe. HapNe infers recent population size fluctuations using either IBD sharing (HapNe-IBD) or linkage disequilibrium (HapNe-LD), which does not require phasing and can be computed in low coverage data, including data sets with heterogeneous sampling times. HapNe shows improved accuracy in a range of simulated demographic scenarios compared to currently available methods for IBD-based and LD-based inference of recent effective population size, while requiring fewer computational resources. We apply HapNe to several modern populations from the 1,000 Genomes Project, the UK Biobank, the Allen Ancient DNA Resource, and recently published samples from Iron Age Britain, detecting multiple instances of recent effective population size variation across these groups.

Dual carbonate clumped isotope (Δ47-Δ48) measurements constrain different sources of kinetic isotope effects and quasi-equilibrium signatures in cave carbonates

Cave carbonate minerals are an important terrestrial paleoclimate archive. A few studies have explored the potential for applying carbonate clumped isotope thermometry to speleothems as a tool for constraining past temperatures. To date, most papers utilizing this method have focused on mass-47 clumped isotope values (Δ47) at a single location and reported that cave carbonate minerals rarely achieve isotopic equilibrium, with kinetic isotope effects (KIEs) attributed to CO2 degassing. More recently, studies have shown that mass-47 and mass-48 CO2 from acid digested carbonate minerals (Δ47 and Δ48) can be used together to assess equilibrium and probe KIEs. Here, we examined 44 natural and synthetic modern cave carbonate mineral samples from 13 localities with varying environmental conditions (ventilation, water level, pCO2, temperature) for (dis)equilibrium using Δ47-Δ48 values, in concert with traditional stable carbon (δ13C) and oxygen (δ18O) isotope ratios. Data showed that 19 of 44 samples exhibited Δ47-Δ48 values indistinguishable from isotopic equilibrium, and 18 (95 %) of these samples yield Δ47-predicted temperatures within error of measured modern temperatures. Conversely, 25 samples exhibited isotopic disequilibria, 13 of which yield erroneous temperature estimates. Within some speleothem samples, we find Δ47-Δ48 values consistent with CO2 degassing effects, however, the majority of samples with KIEs are consistent with other processes being dominant. We hypothesize that these values reflect isotopic buffering effects on clumped isotopes that can be considerable and cannot be overlooked. Using a Raleigh Distillation Model, we examined carbon and oxygen isotope exchange trajectories and their relationships with dual clumped isotope disequilibria. Carbon isotope exchange is associated with depletion of both Δ47 and Δ48 relative to equilibrium, while oxygen isotope exchange is associated with enrichment of both Δ47 and Δ48 relative to equilibrium. Cave rafts collected from proximate locations in Mexico exhibit the largest average departures from equilibrium (ΔΔ47¯ = −0.032 ± 0.007, ΔΔ48¯ = −0.104 ± 0.035, where ΔΔi is the measured value – the equilibrium value). This study shows how the Δ47-Δ48 dual carbonate clumped isotope framework can be applied to a variety of tcave carbonate mineral samples, enabling identification of isotopic equilibria and therefore quantitative application of clumped isotope thermometry for paleoclimate reconstruction, or alternatively, constraining the mechanisms of kinetic effects.

The genomic echoes of the last Green Sahara on the Fulani and Sahelian people

The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics.1,2,3,4,5,6,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world,8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans.1,2,5,6,7,9,10,11,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000-5,000 years before present [BP]).13,14,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes2,16,17,18 and with relevant published ancient sequences (> 1,800 samples).19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events,1,5,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.