Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies—a whole-genome assembly and a regional chromosome assembly—were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional ∼12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Abstract: Approximately 2.4% of the human mitochondrial DNA (mtDNA) genome exhibits common homoplasmic genetic variation. We analyzed 12,975 whole-genome sequences to show that 45.1% of individuals from 1526 mother–offspring pairs harbor a mixed population of mtDNA (heteroplasmy), but the propensity for maternal transmission differs across the mitochondrial genome. Over one generation, we observed selection both for and against variants in specific genomic regions; known variants were more likely to be transmitted than previously unknown variants. However, new heteroplasmies were more likely to match the nuclear genetic ancestry as opposed to the ancestry of the mitochondrial genome on which the mutations occurred, validating our findings in 40,325 individuals. Thus, human mtDNA at the population level is shaped by selective forces within the female germ line under nuclear genetic control, which ensures consistency between the two independent genetic lineages.

Abstract: Coupling between the lower and upper atmosphere, combined with loss of gas from the upper atmosphere to space, likely contributed to the thin, cold, dry atmosphere of modern Mars. To help understand ongoing ion loss to space, the Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft made comprehensive measurements of the Mars upper atmosphere, ionosphere, and interactions with the Sun and solar wind during an interplanetary coronal mass ejection impact in March 2015. Responses include changes in the bow shock and magnetosheath, formation of widespread diffuse aurora, and enhancement of pick-up ions. Observations and models both show an enhancement in escape rate of ions to space during the event. Ion loss during solar events early in Mars history may have been a major contributor to the long-term evolution of the Mars atmosphere.

Abstract: The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability.

Abstract: The global precipitation EOF1 shows a more complex spatial response than the global temperature EOF1, whereas the initial increase in the associated PC1 significantly lags the initial increase in the global temperature PC1 and exhibits greater millennial-scale structure than seen in the global temperature PC1 ( Fig. P1 ). Insofar as precipitation increases should accompany a warming planet, the approximately 2-ky lag between the initial increase in temperature and precipitation may reflect one or more mechanisms that affect low-latitude hydrology, including the impact of Oldest Dryas cooling, a nonlinear response to Northern Hemisphere forcing by insolation and glacial boundary conditions, or interhemispheric latent heat transports. This response may then have been modulated by subsequent millennial-scale changes in the AMOC and its attendant effects on African and Asian monsoon systems and the position of the Intertropical Convergence Zone and North American storm tracks. In contrast, the global temperature PC2 is remarkably similar to a North Atlantic Pa/Th record ( r 2  = 0.86) ( Fig. P1 ) that is interpreted as a kinematic proxy for the strength of the AMOC ( 3 ). Similar millennial-scale variability is identified in several other proxies of intermediate- and deep-ocean circulation, identifying a strong coupling between SSTs and ocean circulation. The large reduction in the AMOC during the Oldest Dryas can be explained as a response to the freshwater forcing associated with the 19-ka meltwater pulse from Northern Hemisphere ice sheets, Heinrich event 1, and routing events along the southern Laurentide Ice Sheet margin, whereas the reduction during the Younger Dryas was likely caused by freshwater routing through the St. Lawrence River and Heinrich event 0. The sustained strength of the AMOC following meltwater pulse 1a supports arguments for a large contribution of this event from Antarctica . With EOF2 accounting for only 13% of deglacial global climate variability, we conclude that the direct global impact of AMOC variations was small in comparison to other processes operating during the last deglaciation. Our analysis indicates that the superposition of two orthogonal modes explains much of the variability (64–100%) in regional and global climate during the last deglaciation ( Fig. P1 ). The nearly uniform spatial pattern of the global temperature EOF1 and the large magnitude of the temperature principal component 1 (PC1) variance indicate that this mode reflects the global warming of the last deglaciation. Given the large global forcing of greenhouse gases (GHGs) ( 2 ), the strong correlation between PC1 and the combined GHG forcing ( r 2  = 0.97) ( Fig. P1 ) supports arguments that GHGs were a major driver of global warming. Fig. P1. ( A ) Comparison of the global temperature PC1 (blue line, with confidence intervals showing results of jackknifing procedure for 68% and 95% of records removed) with record of atmospheric CO 2 from European Project for Ice Coring in Antarctica Dome C ice core (red line with age uncertainty) ( 4 ) on revised timescale from ref.  5 . ( B ) Comparison of the global temperature PC2 (blue line, with confidence intervals showing results of jackknifing procedure for 68% and 95% of records removed) with Pa/Th record (a proxy for Atlantic meridional overturning circulation) ( 3 ) (green and purple symbols). Also shown are freshwater fluxes from ice-sheet meltwater, Heinrich events, and routing events. ( C ) Comparison of the global precipitation PC1 (blue line) with record of methane (green line) and radiative forcing from greenhouse gases (red line). OD, Oldest Dryas; BA, Bølling—Allerød; YD, Younger Dryas; MWP, meltwater pulse. We used empirical orthogonal functions (EOFs) to provide an objective characterization of the temporal and spatial patterns of the leading modes of global surface climate variability for the 20- to 11-ka interval as derived from 166 published proxy records. In addition to characterizing sea surface temperature (SST) variability, we also characterize variability in regional and global continental temperature and precipitation, as well as derive a composite of global temperature variability. The low concentrations of atmospheric CO 2 during the LGM are thought to have been caused by greater storage of carbon in the deep ocean through stratification of the Southern Ocean ( 1 ). Release of the sequestered carbon may have occurred due to deep Southern Ocean overturning induced by enhanced wind-driven upwelling and sea-ice retreat associated with times of Antarctic warming, coincident with the Oldest and Younger Dryas cold events in the north. Several proxies identify large changes in the volume and circulation of the major water masses that fill the deep ocean. During the LGM, there was a marked division in the Atlantic, Indian, and Pacific oceans separating shallower, nutrient-poor intermediate water from more nutrient-rich deep water. In the North Atlantic, Antarctic Bottom Water expanded northward and upward at the expense of North Atlantic Deep Water (NADW), while both water masses maintained a vigorous circulation. In the southwest Pacific and the Arabian Sea, there was an increased influence of Antarctic Intermediate Water (AAIW). During the subsequent deglaciation, there was a net decrease of the Atlantic meridional overturning circulation (AMOC) below LGM strength during the Oldest Dryas, renewed production of NADW at the start of the Bølling–Allerød, followed by a subsequent decrease during the Younger Dryas. In the southwest Pacific and the Arabian Sea, the influence of AAIW further increased during the Oldest Dryas, decreased again during the Bølling–Allerød, and subsequently increased during the Younger Dryas. In contrast, intermediate-depth sites in the southeast Pacific suggest greatest expansion of AAIW during the LGM, followed by stepwise reduction between 17 and 11 ka. Deciphering the evolution of global climate from the end of the Last Glacial Maximum (LGM) approximately 19 ka to the early Holocene 11 ka presents an outstanding opportunity for understanding the transient response of Earth’s climate system to external and internal forcings. During this interval of global warming, virtually every component of the climate system underwent large-scale change, sometimes at extraordinary rates, as the world emerged from the grips of the last ice age. This dramatic time of global change was triggered by changes in insolation, with associated changes in ice sheets, greenhouse gas concentrations, and other amplifying feedbacks that produced distinctive regional and global responses. In addition, there were several episodes of large and rapid sea-level rise and abrupt climate change that produced regional climate signals superposed on those associated with global warming. Considerable ice-sheet melting and sea-level rise occurred after 11 ka, but otherwise the world had entered the current interglaciation with near-pre-Industrial greenhouse gas concentrations and relatively stable climates. Here we summarize a major effort by the paleoclimate research community to characterize these changes through the development of well-dated, high-resolution records of the deep and intermediate ocean as well as surface climate.