Cin-Ty A. Lee

Integrating common and rare genetic variation in diverse human populations.

Despite great progress in identifying genetic variants that influence human disease, most inherited risk remains unexplained. A more complete understanding requires genome-wide studies that fully examine less common alleles in populations with a wide range of ancestry. To inform the design and interpretation of such studies, we genotyped 1.6 million common single nucleotide polymorphisms (SNPs) in 1,184 reference individuals from 11 global populations, and sequenced ten 100-kilobase regions in 692 of these individuals. This integrated data set of common and rare alleles, called ‘HapMap 3’, includes both SNPs and copy number polymorphisms (CNPs). We characterized population-specific differences among low-frequency variants, measured the improvement in imputation accuracy afforded by the larger reference panel, especially in imputing SNPs with a minor allele frequency of ≤5%, and demonstrated the feasibility of imputing newly discovered CNPs and SNPs. This expanded public resource of genome variants in global populations supports deeper interrogation of genomic variation and its role in human disease, and serves as a step towards a high-resolution map of the landscape of human genetic variation.

Continuing Colorado plateau uplift by delamination-style convective lithospheric downwelling

The Colorado plateau is a large, tectonically intact, physiographic province in the southwestern North American Cordillera that stands at ∼1,800–2,000 m elevation and has long been thought to be in isostatic equilibrium. The origin of these high elevations is unclear because unlike the surrounding provinces, which have undergone significant Cretaceous–Palaeogene compressional deformation followed by Neogene extensional deformation, the Colorado plateau is largely internally undeformed. Here we combine new seismic tomography and receiver function images to resolve a vertical high-seismic-velocity anomaly beneath the west-central plateau that extends more than 200 km in depth. The upper surface of this anomaly is seismically defined by a dipping interface extending from the lower crust to depths of 70–90 km. The base of the continental crust above the anomaly has a similar shape, with an elevated Moho. We interpret these seismic structures as a continuing regional, delamination-style foundering of lower crust and continental lithosphere. This implies that Pliocene (2.6–5.3 Myr ago) uplift of the plateau and the magmatism on its margins are intimately tied to continuing deep lithospheric processes. Petrologic and geochemical observations indicate that late Cretaceous–Palaeogene (∼90–40 Myr ago) low-angle subduction hydrated and probably weakened much of the Proterozoic tectospheric mantle beneath the Colorado plateau. We suggest that mid-Cenozoic (∼35–25 Myr ago) to Recent magmatic infiltration subsequently imparted negative compositional buoyancy to the base and sides of the Colorado plateau upper mantle, triggering downwelling. The patterns of magmatic activity suggest that previous such events have progressively removed the Colorado plateau lithosphere inward from its margins, and have driven uplift. Using Grand Canyon incision rates and Pliocene basaltic volcanism patterns, we suggest that this particular event has been active over the past ∼6 Myr.

Copper Systematics in Arc Magmas and Implications for Crust-Mantle Differentiation

Copper-Bottomed Crust The formation of volcanic arc chains near subduction zones brings large amounts of magma from the upper mantle to the crust, contributing to the formation of island chains in the ocean and adding material to continents. Over time, arc magmas also contribute indirectly to the composition of the oceans and atmosphere through outgassing and weathering of volcanic minerals; however, it is unclear what determines the oxidized nature of arc magmas themselves. Lee et al. (p. 64) measured Cu contents in a range of arc-derived volcanic rocks as a proxy for arc magma redox states. An overall depletion of Cu, which is sensitive to reduced sulfur contents, in global continental crust suggests that there is a hidden reservoir of copper-rich sulfides deep in Earths interior. The copper contents of magmas imply that the formation of sulfide-bearing cumulates under reducing conditions is a critical step in the formation of continental crust. Arc magmas are important building blocks of the continental crust. Because many arc lavas are oxidized, continent formation is thought to be associated with oxidizing conditions. On the basis of copper’s (Cu’s) affinity for reduced sulfur phases, we tracked the redox state of arc magmas from mantle source to emplacement in the crust. Primary arc and mid-ocean ridge basalts have identical Cu contents, indicating that the redox states of primitive arc magmas are indistinguishable from that of mid-ocean ridge basalts. During magmatic differentiation, the Cu content of most arc magmas decreases markedly because of sulfide segregation. Because a similar depletion in Cu characterizes global continental crust, the formation of sulfide-bearing cumulates under reducing conditions may be a critical step in continent formation.

RE-OS SYSTEMATICS OF MANTLE XENOLITHS FROM THE EAST AFRICAN RIFT : AGE, STRUCTURE, AND HISTORY OF THE TANZANIAN CRATON

In order to understand the effects of contractional and extensional tectonics on thick, mantle roots, we have undertaken a systematic study of mantle xenoliths from the Labait volcano, which lies within the East African Rift on the eastern boundary of the Archean Tanzanian craton. The Re-Os systematics of the Labait xenoliths show that ancient, refractory lithosphere is present to depths of ;140 km. Above this depth, the mantle section consists of harzburgitic xenoliths with whole rock 187 Os/ 188 Os between 0.1081 and 0.1140, corresponding to Re depletion (TRD) ages of 2.8 to 2.0 Ga. Chromites from these samples are generally less radiogenic than their corresponding whole rocks and have TRD ages between 2.5 to 2.9 Ga, yielding the best estimate for the age of this portion of the lithosphere. Coupled petrographic and isotopic data for some of these samples indicate they have been variably overprinted by recent addition of Re and/or radiogenic Os. Between 4.4 to 4.7 GPa (;140 to 150 km depth), peridotites are more fertile and yield younger TRD ages (1.0 Ga to future ages). The highest temperature sample has radiogenic 187 Os/ 188 Os (0.133), overlapping the range measured for metasomatic xenoliths and the Labait host melilitite (0.13 to 0.14). This range is taken to represent asthenospheric mantle beneath the Tanzanian craton, which has plume-like isotopic characteristics. The suite shows a good correlation on 187 Os/ 188 Os vs. temperature (hence depth) and 187 Os/ 188 Os vs. wt.% Al2O3 or CaO plots. These trends, which pass above primitive mantle compositions, may reflect mixing of recent plume-derived Os with ancient lithospheric Os, formation of the lowest portion of the lithosphere during successive melting events or a combination of both processes. Our data show that complete delamination of the lithospheric mantle has not occurred beneath the Tanzanian craton during its long tectonic history. However, if the Archean lithosphere was originally thicker than the ;140 km currently beneath Labait, then the lithosphere has been thinned, either by thermal erosion associated with the rift or by partial delamination during Proterozoic collision. Finally, we see no evidence for extensive lithospheric thinning associated with development of the East African Rift, although overprinting of the lithosphere by rift-related magmas has occurred. Copyright

Preservation of ancient and fertile lithospheric mantle beneath the southwestern United States

Stable continental regions, free from tectonic activity, are generally found only within ancient cratons—the centres of continents which formed in the Archaean era, 4.0–2.5 Gyr ago. But in the Cordilleran mountain belt of western North America some younger (middle Proterozoic) regions have remained stable, whereas some older (late Archaean) regions have been tectonically disturbed, suggesting that age alone does not determine lithospheric strength and crustal stability. Here we report rhenium–osmium isotope and mineral compositions of peridotite xenoliths from two regions of the Cordilleran mountain belt. We found that the younger, undeformed Colorado plateau is underlain by lithospheric mantle that is ‘depleted’ (deficient in minerals extracted by partial melting of the rock), whereas the older (Archaean), yet deformed, southern Basin and Range province is underlain by ‘fertile’ lithospheric mantle (not depleted by melt extraction). We suggest that the apparent relationship between composition and lithospheric strength, inferred from different degrees of crustal deformation, occurs because depleted mantle is intrinsically less dense than fertile mantle (due to iron having been lost when melt was extracted from the rock). This allows the depleted mantle to form a thicker thermal boundary layer between the deep convecting mantle and the crust, thus reducing tectonic activity at the surface. The inference that not all Archaean crust developed a strong and thick thermal boundary layer leads to the possibility that such ancient crust may have been overlooked because of its intensive reworking or lost from the geological record owing to preferential recycling.

The redox state of arc mantle using Zn/Fe systematics

Many arc lavas are more oxidized than mid-ocean-ridge basalts and subduction introduces oxidized components into the mantle. As a consequence, the sub-arc mantle wedge is widely believed to be oxidized. The Fe oxidation state of sub-arc mantle is, however, difficult to determine directly, and debate persists as to whether this oxidation is intrinsic to the mantle source. Here we show that Zn/FeT (where FeT = Fe2+ + Fe3+) is redox-sensitive and retains a memory of the valence state of Fe in primary arc basalts and their mantle sources. During melting of mantle peridotite, Fe2+ and Zn behave similarly, but because Fe3+ is more incompatible than Fe2+, melts generated in oxidized environments have low Zn/FeT. Primitive arc magmas have identical Zn/FeT to mid-ocean-ridge basalts, suggesting that primary mantle melts in arcs and ridges have similar Fe oxidation states. The constancy of Zn/FeT during early differentiation involving olivine requires that Fe3+/FeT remains low in the magma. Only after progressive fractionation does Fe3+/FeT increase and stabilize magnetite as a fractionating phase. These results suggest that subduction of oxidized crustal material may not significantly alter the redox state of the mantle wedge. Thus, the higher oxidation states of arc lavas must be in part a consequence of shallow-level differentiation processes, though such processes remain poorly understood.

Upside-down differentiation and generation of a primordial lower mantle

Except for the first 50–100 million years or so of the Earth’s history, when most of the mantle may have been subjected to melting, the differentiation of Earth’s silicate mantle has been controlled by solid-state convection. As the mantle upwells and decompresses across its solidus, it partially melts. These low-density melts rise to the surface and form the continental and oceanic crusts, driving the differentiation of the silicate part of the Earth. Because many trace elements, such as heat-producing U, Th and K, as well as the noble gases, preferentially partition into melts (here referred to as incompatible elements), melt extraction concentrates these elements into the crust (or atmosphere in the case of noble gases), where nearly half of the Earth’s budget of these elements now resides. In contrast, the upper mantle, as sampled by mid-ocean ridge basalts, is highly depleted in incompatible elements, suggesting a complementary relationship with the crust. Mass balance arguments require that the other half of these incompatible elements be hidden in the Earth’s interior. Hypotheses abound for the origin of this hidden reservoir. The most widely held view has been that this hidden reservoir represents primordial material never processed by melting or degassing. Here, we suggest that a necessary by-product of whole-mantle convection during the Earth’s first billion years is deep and hot melting, resulting in the generation of dense liquids that crystallized and sank into the lower mantle. These sunken lithologies would have ‘primordial’ chemical signatures despite a non-primordial origin.

Radar-Enabled Recovery of the Sutter’s Mill Meteorite, a Carbonaceous Chondrite Regolith Breccia

The Meteor That Fell to Earth In April 2012, a meteor was witnessed over the Sierra Nevada Mountains in California. Jenniskens et al. (p. 1583) used a combination of photographic and video images of the fireball coupled with Doppler weather radar images to facilitate the rapid recovery of meteorite fragments. A comprehensive analysis of some of these fragments shows that the Sutters Mill meteorite represents a new type of carbonaceous chondrite, a rare and primitive class of meteorites that contain clues to the origin and evolution of primitive materials in the solar system. The unexpected and complex nature of the fragments suggests that the surfaces of C-class asteroids, the presumed parent bodies of carbonaceous chondrites, are more complex than previously assumed. Analysis of this rare meteorite implies that the surfaces of C-class asteroids can be more complex than previously assumed. Doppler weather radar imaging enabled the rapid recovery of the Sutter’s Mill meteorite after a rare 4-kiloton of TNT–equivalent asteroid impact over the foothills of the Sierra Nevada in northern California. The recovered meteorites survived a record high-speed entry of 28.6 kilometers per second from an orbit close to that of Jupiter-family comets (Tisserand’s parameter = 2.8 ± 0.3). Sutter’s Mill is a regolith breccia composed of CM (Mighei)–type carbonaceous chondrite and highly reduced xenolithic materials. It exhibits considerable diversity of mineralogy, petrography, and isotope and organic chemistry, resulting from a complex formation history of the parent body surface. That diversity is quickly masked by alteration once in the terrestrial environment but will need to be considered when samples returned by missions to C-class asteroids are interpreted.

Geochemical/Petrologic Constraints on the Origin of Cratonic Mantle

Cratons are underlain by thick, cold, and highly melt-depleted mantle roots, the latter imposing a chemical buoyancy that roughly offsets the cratons negative thermal buoyancy associated with its cooler thermal state. Petrologic/geochemical predictions of three endmember scenarios for the origin of cratonic mantle are discussed: (1) high-degree melting in a very hot plume head with a potential temperature >1650°C, (2) accretion of oceanic lithosphere, and (3) accretion of arc lithosphere. The hot plume scenario predicts that cratonic peridotites were formed by high degrees of melting at very high pressures (>7 GPa), whereas the two accretion scenarios predict an origin by melting on average at lower pressures (<∼4 GPa) followed by subsequent transport of these residual peridotites to the greater depths (3-7 GPa) from which they presently derive. Major-element and mildly incompatible trace-element compositions of cratonic peridotite xenoliths suggest a low pressure origin, favoring the two accretion scenarios. The two accretion scenarios are difficult to distinguish geochemically, but one difference is that garnet pyroxenite xenoliths might be more clinopyroxene- and Si-rich in arc environments than in oceanic environments, which would be more olivine-rich (and Si-poor) due to lower pressures of crystallization in oceanic settings compared to arc settings. High-MgO cratonic garnet pyroxenite xenoliths in fact have major-element systematics similar to high-MgO garnet pyroxenites from Phanerozoic continental arcs. Taken at face value, this suggests that at least some component of cratons may have formed by accretion of arc lithosphere. Low-MgO garnet pyroxenite xenoliths from cratons represent either subducted oceanic crust or arc basalts. Cratonic mantle may be formed by a combination of arc and oceanic lithospheric mantle accretion.

Deep lithospheric dynamics beneath the Sierra Nevada during the Mesozoic and Cenozoic as inferred from xenolith petrology

[1] Abstract: Peridotite xenoliths erupted in late Miocene basalts (� 8 Ma) in the central Sierra Nevada sample a lithosphere that is vertically stratified in terms of age and thermal history. The deeper portions (� 45– 100 km) have asthenospheric osmium isotopic compositons and possess textural and chemical evidence for cooling from >11008 to 700– 8208C. The shallower portions (<60 km) have unradiogenic Os isotopic compositions, which yield Proterozoic model ages, and contain orthopyroxenes that record temperatures as low as 6708C in their cores and heating up to 9008C on their rims. These observations suggest that the deeper xenoliths represent fragments of hot asthenosphere that upwelled to intrude and/or underplate the overlying Proterozoic lithosphere represented by the shallower xenoliths. The contrasting thermal histories between the shallow and deep xenoliths suggest that hot asthenosphere and cold lithosphere were suddenly juxtaposed, a feature consistent with the aftermath of rapid lithospheric removal or sudden intrusion of asthenospheric mantle into the lithosphere rather than passive extension. On the basis of regional tectonics and various time constraints, it is possible that this lithospheric removal event was associated with the generation of the Sierra Nevada granitic batholith during Mesozoic subduction of the Farallon plate beneath North America. Pleistocene basalt-hosted xenoliths record a different chapter in the geodynamic history of the Sierras. These xenoliths are relatively fertile, come from depths shallower than 45– 60 km, are characterized by asthenospheric Os isotopic compositions, record hot equilibration temperatures (10008– 11008C), and show no evidence for cooling. The strong contrast in composition and thermal history between the Pleistocene and late Miocene suites indicate that the post-Mesozoic lithospheric mantle, as represented by the latter, was entirely replaced by the former. The hot Pleistocene peridotites may thus represent new lithospheric additions associated witha post-Miocene lith osph eric removal event or extension. Highelevations, low sub-Moho seismic velocities, and the presence of fast velocity anomalies at 200 km depth may be manifestations of this event. If lithospheric removal occurred in the Mesozoic and Cenozoic, the observations presented here place constraints on the styles of lithospheric removal. In the Mesozoic, the lithospheric mantle was only partially removed, whereas in the Pliocene, the entire lithospheric mantle and probably the mafic lower crust were removed.