European and African descendants settled the continental US during the 17th-19th centuries, coming into contact with established Native American populations. The resulting admixture among these ...groups yielded a significant reservoir of Native American ancestry in the modern US population. We analyzed the patterns of Native American admixture seen for the three largest genetic ancestry groups in the US population: African descendants, Western European descendants, and Spanish descendants. The three groups show distinct Native American ancestry profiles, which are indicative of their historical patterns of migration and settlement across the country. Native American ancestry in the modern African descendant population does not coincide with local geography, instead forming a single group with origins in the southeastern US, consistent with the Great Migration of the early 20th century. Western European descendants show Native American ancestry that tracks their geographic origins across the US, indicative of ongoing contact during westward expansion, and Native American ancestry can resolve Spanish descendant individuals into distinct local groups formed by more recent migration from Mexico and Puerto Rico. We found an anomalous pattern of Native American ancestry from the US southwest, which most likely corresponds to the Nuevomexicano descendants of early Spanish settlers to the region. We addressed a number of controversies surrounding this population, including the extent of Sephardic Jewish ancestry. Nuevomexicanos are less admixed than nearby Mexican-American individuals, with more European and less Native American and African ancestry, and while they do show demonstrable Sephardic Jewish ancestry, the fraction is no greater than seen for other New World Spanish descendant populations.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In this paper, we discuss the results of 2000–2100 simulations following the emissions associated with the Representative Concentration Pathways (RCPs) with a chemistry-climate model, focusing on the ...changes in 1) atmospheric composition (troposphere and stratosphere) and 2) associated environmental parameters (such as nitrogen deposition). In particular, we find that tropospheric ozone is projected to decrease (RCP2.6, RCP4.5 and RCP6) or increase (RCP8.5) between 2000 and 2100, with variations in methane a strong contributor to this spread. The associated tropospheric ozone global radiative forcing is shown to be in agreement with the estimate used in the RCPs, except for RCP8.5. Surface ozone in 2100 is projected to change little compared from its 2000 distribution, a much-reduced impact from previous projections based on the A2 high-emission scenario. In addition, globally-averaged stratospheric ozone is projected to recover at or beyond pre-1980 levels. Anthropogenic aerosols are projected to strongly decrease in the 21st century, a reflection of their projected decrease in emissions. Consequently, sulfate deposition is projected to strongly decrease. However, nitrogen deposition is projected to increase over certain regions because of the projected increase in NH
3
emissions.
Climate simulations that consider injection into the atmosphere of 15,000 Tg of soot, the amount estimated to be present at the Cretaceous−Paleogene boundary, produce what might have been one of the ...largest episodes of transient climate change in Earth history. The observed soot is believed to originate from global wildfires ignited after the impact of a 10-km-diameter asteroid on the Yucatán Peninsula 66 million y ago. Following injection into the atmosphere, the soot is heated by sunlight and lofted to great heights, resulting in a worldwide soot aerosol layer that lasts several years. As a result, little or no sunlight reaches the surface for over a year, such that photosynthesis is impossible and continents and oceans cool by as much as 28 °C and 11 °C, respectively. The absorption of light by the soot heats the upper atmosphere by hundreds of degrees. These high temperatures, together with a massive injection of water, which is a source of odd-hydrogen radicals, destroy the stratospheric ozone layer, such that Earth’s surface receives high doses of UV radiation for about a year once the soot clears, five years after the impact. Temperatures remain above freezing in the oceans, coastal areas, and parts of the Tropics, but photosynthesis is severely inhibited for the first 1 y to 2 y, and freezing temperatures persist at middle latitudes for 3 y to 4 y. Refugia from these effects would have been very limited. The transient climate perturbation ends abruptly as the stratosphere cools and becomes supersaturated, causing rapid dehydration that removes all remaining soot via wet deposition.
The role of stratospheric water vapor (SWV) changes, in response to increasing
CO
2
, as a feedback component of quantitative significance for climate sensitivity has remained controversial. Here, we ...calculate the SWV climate feedback under abrupt
CO
2
quadrupling in the CMIP5 ensemble of models. All models robustly show a moistening of the stratosphere, causing a global mean net stratosphere adjusted radiative perturbation of
0.89
±
0.27
Wm
-
2
at the reference tropopause. The stratospheric temperature adjustment is a crucial component of this radiative perturbation. The associated climate feedback is
0.17
±
0.05
Wm
-
2
K
-
1
, with a considerable inter-model range of 0.12–0.28
Wm
-
2
K
-
1
. Taking into account the rise in tropopause height under
4
×
CO
2
slightly reduces the feedback to
0.15
±
0.04
Wm
-
2
K
-
1
, with a range of 0.10–
0.26
Wm
-
2
K
-
1
. The SWV radiative perturbation peaks in the midlatitudes and not the tropics: this is due primarily to increases in SWV in the extratropical lowermost stratosphere, which cause the majority (over three quarters) of the global mean feedback. Based on these results, we suggest an increased focus on understanding drivers of water vapor trends in the extratropical lowermost stratosphere. We conclude that the SWV feedback is important, being on the same order of magnitude as the global mean surface albedo and cloud feedbacks in the multi-model mean.
Modern Latin American populations were formed via genetic admixture among ancestral source populations from Africa, the Americas and Europe. We are interested in studying how combinations of genetic ...ancestry in admixed Latin American populations may impact genomic determinants of health and disease. For this study, we characterized the impact of ancestry and admixture on genetic variants that underlie health- and disease-related phenotypes in population genomic samples from Colombia, Mexico, Peru, and Puerto Rico.
We analyzed a total of 347 admixed Latin American genomes along with 1102 putative ancestral source genomes from Africans, Europeans, and Native Americans. We characterized the genetic ancestry, relatedness, and admixture patterns for each of the admixed Latin American genomes, finding a spectrum of ancestry proportions within and between populations. We then identified single nucleotide polymorphisms (SNPs) with anomalous ancestry-enrichment patterns, i.e. SNPs that exist in any given Latin American population at a higher frequency than expected based on the population's genetic ancestry profile. For this set of ancestry-enriched SNPs, we inspected their phenotypic impact on disease, metabolism, and the immune system. All four of the Latin American populations show ancestry-enrichment for a number of shared pathways, yielding evidence of similar selection pressures on these populations during their evolution. For example, all four populations show ancestry-enriched SNPs in multiple genes from immune system pathways, such as the cytokine receptor interaction, T cell receptor signaling, and antigen presentation pathways. We also found SNPs with excess African or European ancestry that are associated with ancestry-specific gene expression patterns and play crucial roles in the immune system and infectious disease responses. Genes from both the innate and adaptive immune system were found to be regulated by ancestry-enriched SNPs with population-specific regulatory effects.
Ancestry-enriched SNPs in Latin American populations have a substantial effect on health- and disease-related phenotypes. The concordant impact observed for same phenotypes across populations points to a process of adaptive introgression, whereby ancestry-enriched SNPs with specific functional utility appear to have been retained in modern populations by virtue of their effects on health and fitness.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesize that admixture can enable rapid adaptive evolution in human populations by ...introducing novel genetic variants (haplotypes) at intermediate frequencies, and we test this hypothesis through the analysis of whole genome sequences sampled from admixed Latin American populations in Colombia, Mexico, Peru, and Puerto Rico.
Our screen for admixture-enabled selection relies on the identification of loci that contain more or less ancestry from a given source population than would be expected given the genome-wide ancestry frequencies. We employ a combined evidence approach to evaluate levels of ancestry enrichment at single loci across multiple populations and multiple loci that function together to encode polygenic traits. We find cross-population signals of African ancestry enrichment at the major histocompatibility locus on chromosome 6, consistent with admixture-enabled selection for enhanced adaptive immune response. Several of the human leukocyte antigen genes at this locus, such as HLA-A, HLA-DRB51, and HLA-DRB5, show independent evidence of positive selection prior to admixture, based on extended haplotype homozygosity in African populations. A number of traits related to inflammation, blood metabolites, and both the innate and adaptive immune system show evidence of admixture-enabled polygenic selection in Latin American populations.
The results reported here, considered together with the ubiquity of admixture in human evolution, suggest that admixture serves as a fundamental mechanism that drives rapid adaptive evolution in human populations.
Accurate representation of global stratospheric aerosols from volcanic and nonvolcanic sulfur emissions is key to understanding the cooling effects and ozone losses that may be linked to volcanic ...activity. Attribution of climate variability to volcanic activity is of particular interest in relation to the post‐2000 slowing in the rate of global average temperature increases. We have compiled a database of volcanic SO2 emissions and plume altitudes for eruptions from 1990 to 2014 and developed a new prognostic capability for simulating stratospheric sulfate aerosols in the Community Earth System Model. We used these combined with other nonvolcanic emissions of sulfur sources to reconstruct global aerosol properties from 1990 to 2014. Our calculations show remarkable agreement with ground‐based lidar observations of stratospheric aerosol optical depth (SAOD) and with in situ measurements of stratospheric aerosol surface area density (SAD). These properties are key parameters in calculating the radiative and chemical effects of stratospheric aerosols. Our SAOD calculations represent a clear improvement over available satellite‐based analyses, which generally ignore aerosol extinction below 15 km, a region that can contain the vast majority of stratospheric aerosol extinction at middle and high latitudes. Our SAD calculations greatly improve on that provided for the Chemistry‐Climate Model Initiative, which misses about 60% of the SAD measured in situ on average during both volcanically active and volcanically quiescent periods.
Key Points
We developed a global aerosol reconstruction for 1990‐2014 using CESM1(WACCM) and volcanic emissions
Satellite‐based forcing data neglect 50‐95% of extratropical stratospheric aerosol
Our output agrees much better with in situ and ground‐based observations than standard forcing data
Pharmacogenomic (PGx) variants mediate how individuals respond to medication, and response differences among racial/ethnic groups have been attributed to patterns of PGx diversity. We hypothesized ...that genetic ancestry (GA) would provide higher resolution for stratifying PGx risk, since it serves as a more reliable surrogate for genetic diversity than self-identified race/ethnicity (SIRE), which includes a substantial social component. We analyzed a cohort of 8628 individuals from the United States (US), for whom we had both SIRE information and whole genome genotypes, with a focus on the three largest SIRE groups in the US: White, Black (African-American), and Hispanic (Latino). Our approach to the question of PGx risk stratification entailed the integration of two distinct methodologies: population genetics and evidence-based medicine. This integrated approach allowed us to consider the clinical implications for the observed patterns of PGx variation found within and between population groups.
Whole genome genotypes were used to characterize individuals' continental ancestry fractions-European, African, and Native American-and individuals were grouped according to their GA profiles. SIRE and GA groups were found to be highly concordant. Continental ancestry predicts individuals' SIRE with > 96% accuracy, and accordingly, GA provides only a marginal increase in resolution for PGx risk stratification. In light of the concordance between SIRE and GA, taken together with the fact that information on SIRE is readily available to clinicians, we evaluated PGx variation between SIRE groups to explore the potential clinical utility of race and ethnicity. PGx variants are highly diverged compared to the genomic background; 82 variants show significant frequency differences among SIRE groups, and genome-wide patterns of PGx variation are almost entirely concordant with SIRE. The vast majority of PGx variation is found within rather than between groups, a well-established fact for almost all genetic variants, which is often taken to argue against the clinical utility of population stratification. Nevertheless, analysis of highly differentiated PGx variants illustrates how SIRE partitions PGx variation based on groups' characteristic ancestry patterns. These cases underscore the extent to which SIRE carries clinically valuable information for stratifying PGx risk among populations, albeit with less utility for predicting individual-level PGx alleles (genotypes), supporting the concept of population pharmacogenomics.
Perhaps most interestingly, we show that individuals who identify as Black or Hispanic stand to gain far more from the consideration of race/ethnicity in treatment decisions than individuals from the majority White population.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
An overview of a simulation referred to as the ‘‘Last Millennium’’ (LM) simulation of the Community Climate System Model, version 4 (CCSM4), is presented. The CCSM4 LM simulation reproduces many ...large-scale climate patterns suggested by historical and proxy-data records, with Northern Hemisphere (NH) and Southern Hemisphere (SH) surface temperatures cooling to the early 1800s Common Era by ∼0.5°C (NH) and ∼0.3°C (SH), followed by warming to the present. High latitudes of both hemispheres show polar amplification of the cooling from the Medieval Climate Anomaly (MCA) to the Little Ice Age (LIA) associated with sea ice increases. The LM simulation does not reproduce La Niña–like cooling in the eastern Pacific Ocean during the MCA relative to the LIA, as has been suggested by proxy reconstructions. Still, dry medieval conditions over the southwestern and central United States are simulated in agreement with proxy indicators for these regions. Strong global cooling is associated with large volcanic eruptions, with indications of multidecadal colder climate in response to larger eruptions. The CCSM4’s response to large volcanic eruptions captures some reconstructed patterns of temperature changes over Europe and North America, but not those of precipitation in the Asian monsoon region. The Atlantic multidecadal oscillation (AMO) has higher variance at centennial periods in the LM simulation compared to the 1850 nontransient run, suggesting a long-term Atlantic Ocean response to natural forcings. The North Atlantic Oscillation (NAO), Pacific decadal oscillation (PDO), and El Niño–Southern Oscillation (ENSO) variability modes show little or no change. CCSM4 does not simulate a persistent positive NAO or a prolonged period of negative PDO during the MCA, as suggested by some proxy reconstructions.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Community Earth System Model version 2 (CESM2) includes a detailed representation of chemistry throughout the atmosphere in the Community Atmosphere Model with chemistry and Whole Atmosphere ...Community Climate Model configurations. These model configurations use the Model for Ozone and Related chemical Tracers (MOZART) family of chemical mechanisms, covering the troposphere, stratosphere, mesosphere, and lower thermosphere. The new MOZART tropospheric chemistry scheme (T1) has a number of updates over the previous version (MOZART‐4) in CESM, including improvements to the oxidation of isoprene and terpenes, organic nitrate speciation, and aromatic speciation and oxidation and thus improved representation of ozone and secondary organic aerosol precursors. An evaluation of the present‐day simulations of CESM2 being provided for Climate Model Intercomparison Project round 6 (CMIP6) is presented. These simulations, using the anthropogenic and biomass burning emissions from the inventories specified for CMIP6, as well as online calculation of emissions of biogenic compounds, lightning NO, dust, and sea salt, indicate an underestimate of anthropogenic emissions of a variety of compounds, including carbon monoxide and hydrocarbons. The simulation of surface ozone in the southeast United States is improved over previous model versions, largely due to the improved representation of reactive nitrogen and organic nitrate compounds resulting in a lower ozone production rate than in CESM1 but still overestimates observations in summer. The simulation of tropospheric ozone agrees well with ozonesonde observations in many parts of the globe. The comparison of NOx and PAN to aircraft observations indicates the model simulates the nitrogen budget well.
Plain Language Summary
The set of chemical reactions for tropospheric chemistry used in the Community Earth System Model version 2 (CESM2) has been updated significantly over CESM1 in the Community Atmosphere Model with chemistry (CAM‐chem) and Whole Atmosphere Community Climate Model (WACCM) configurations. The emissions used for the CESM2 simulations are documented here, with anthropogenic and biomass burning emissions based on the specified inventories for Climate Model Intercomparison Project 6 (CMIP6), and emissions of biogenic compounds, lightning NO, dust, and sea salt are calculated online and dependent on the simulated meteorology. Evaluation of the CAM‐chem and WACCM configurations of CESM2 with observations indicate an underestimate of anthropogenic emissions of a variety of compounds, including carbon monoxide and hydrocarbons. The updated chemistry leads to an improvement in the simulation of tropospheric ozone.
Key Points
This paper fully documents the significant updates to the chemistry mechanisms in version 2 of the Community Earth System Model
The new tropospheric chemistry scheme improves representation of isoprene oxidation as well as other ozone precursors over earlier versions
The simulation of tropospheric ozone is improved in comparison to observations
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