Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep learning reveals the role of copy number variation in the genetic architecture of a highly polymorphic sexual trait

The extraordinary variation in male guppy coloration has proven a powerful model for studying the interplay of natural and sexual selection. Many guppy populations exhibit substantial Y-linkage of color traits, and this has hampered the identification of the genetic architecture underlying male guppy color, as well as clouded our understanding of how this exceptional level of diversity is maintained. Here we identify the heritability and genetic basis of male color variation using convolutional neural networks for high-resolution phenotyping coupled with selection experiments, controlled pedigrees and whole-genome resequencing for a Genome Wide Association Study (GWAS) of color. Our phenotypic and genomic results converge to show that color patterning in guppies is a combination of many heritable features, each with a partially overlapping genetic architecture spanning the entire genome. Unusually, our GWAS results suggest that copy number variation, particularly copies shared between the Y chromosome and the remainder of the genome, is responsible for much of the variation in color in guppies, providing a potential mechanism for the maintenance of variation of this classic model trait.
A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

The Notomicrus traili species group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed to N. traili and the closely related N. gracilipes recovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within the N. traili group. First, we use short-read whole genome sequencing of four noterid genera to design a noterid-specific UCE probe set (Noteridae 3.4Kv1) targeting over 3,400 unique loci. Using this probe set, we capture UCE data from population-level sampling of 44 traili group specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putative N. traili group populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within the traili group that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co-ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of the traili group in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow-scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.
Replicated Functional Evolution in Cichlid Adaptive Radiations

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Tanganyika, Malawi and Victoria) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than in Lake Tanganyika, despite being at least 25 My older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting, at least for lake radiations, extremely rapid trait evolution at early stages. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.
Approaches for defining thresholds and return periods for rainfall‐triggered shallow landslides

Probabilistic thresholds for triggering shallow landslides by rainfall are developed using two approaches: a logistic regression model and Iverson's physically based model. Both approaches are applied to a 180 km2 area in northern Italy. For the physically based model a Monte Carlo approach is used to obtain probabilities of slope failure associated with differing combinations of rainfall intensity and duration as well as differing topographic settings. For the logistic regression model hourly and daily rainfall data and split‐sample testing are used to explore the effect of antecedent rainfall on triggering thresholds. It is demonstrated that both the statistical and physically based models provide stochastic thresholds that express the probability of landslide triggering. The resulting thresholds are comparable, even though the two approaches are conceptually different. The physically based model also provides an estimate of the percentage of potentially unstable areas in which failure can be triggered with a certain probability. The return period of rainfall responsible for landslide triggering is studied by using a Gumbel scaling model of rainfall intensity–duration–frequency curves. It is demonstrated that antecedent rainfall must be taken into account in landslide forecasting, and a method is proposed to correct the rainfall return period by filtering the rainfall maxima with a fixed threshold of antecedent rainfall. This correction produces an increase of the return periods, especially for rainstorms of short duration. Copyright © 2009 John Wiley & Sons, Ltd.
Rapid and Widespread Generation of Recent Oolitic Hardgrounds on a High Energy Bahamian Platform, Eleuthera Bank, Bahamas

ABSTRACT Contemporary intergranular submarine cementation occurs in close association with strongly agitated oolitic sands in the Schooner Cays tidal bar belt, resulting in widespread generation of surficial oolitic hardgrounds. Hardground formation takes place from near the shelf margin bankward up to 15-17 kilometers, within the zone of active oolitic sand, in water depths ranging from 1-II meters. Two forms of lithified oolitic sediment (hardgrounds) are recognized: in situ surficial crusts and unattached clasts (erosional crust fragments). Isopachous fibrous aragonite constitutes the major physicochemical cement; other cement forms of aragonite and high magnesium calcite are widespread but subordinate. Previously undocumented, probable chasmolithic/endolithic algae also effectively bind and cement surficial unconsolidated oolitic sediment by filament calcification. Characteristic decrease in cementation downward from crust surfaces substantiates their formation at or near the sediment-water interface. Patterns of hardground formation apparently result from the interaction of tidal bar surface topography, local hydrography and stabilization by algal scum mats. Radiocarbon dating, field relationships and crust petrography document the rapid and contemporaneous formation of oolitic hardgrounds. Initial crust formation can occur within a few months or less. Hand probing of tidal bars and radiocarbon dating of erosional oolitic clasts suggest that similar patterns of hardground formation occurred during earlier growth stages of the tidal bars.
A formal semantics of C with applications

This paper describes an executable formal semantics of C expressed using a formalism based on term rewriting. Being executable, the semantics has been thoroughly tested against the GCC torture test suite and successfully passes over 96% of 715 test programs. It is the most complete and thoroughly tested formal definition of C to date. The semantics yields an interpreter, debugger, and state space search tool “for free”. The semantics is shown capable of automatically finding program errors, both statically and at runtime. It is also used to enumerate nondeterministic behavior. These techniques together allow the tool to identify undefined programs. The entire C semantics is included as Appendix B.
Improved Os‐isotope stratigraphy of the Arctic Ocean

The history of the Arctic Ocean remained poorly known until the 2004 IODP coring of Lomonosov Ridge sediments. Early studies of the recovered sequence demonstrated the existence of an Eocene ‘lake‐stage’ prior to the transition to marine conditions. The marine stage onset was inferred to be ∼17.5 million years ‐Ma‐ ago, thus implying a nearly 26 Ma gap between the lacustrine and marine episodes, and an unusual tectonic history for Lomonosov Ridge, in order to explain this gap. More recently, Rhenium‐Osmium (Re‐Os) isotope measurements of the transition from the lacustrine to marine sediments suggested a much earlier inception of marine conditions and the absence of any significant gap between both episodes. Here, an improved Osmium isotope stratigraphy and Re‐Os data concur to assign a Late Eocene age (∼36 Ma) to the marine invasion, consistent with a relative change in sea level on top of Lomonosov ridge, either from tectonic origin or from another cause.
Anthropogenic and solar components of hemispheric 14C

A variable solar (helio‐magnetic) modulation of the cosmic ray flux causes atmospheric 14C to change on a decadal to century timescale. Ocean‐atmosphere exchange rates and atmospheric circulation patterns play a role in Northern‐Southern Hemispheric 14C offsets and regional 14C differences that are significant for radiocarbon dating. Time dependent radiocarbon age differences, relative to Washington, were determined for Alaska (A.D. 1884–1932), South Chile (A.D. 1850–1952 and A.D. 1670–1722), Tasmania (A.D. 1895–1950) and Siberia (A.D. 1545–1715). Twentieth century fossil fuel CO2, lacking 14C and mostly released in the Northern Hemisphere (N), has entered the Southern Hemisphere (S) by atmospheric N‐S exchange. Regional 14C time series show that initial (19th century) positive N‐S 14C offsets switch to negative values by AD 1940. First order carbon reservoir modeling predicts such crossovers.
Consumer financial literacy and the efficiency of Consumer financial literacy and the efficiency of mortgage ‐ related decisions: New evidence from the Panel Study mortgage related decisions: New evidence from the Panel Study of Income Dynamics of Income Dynamics

This study evaluated the link between financial literacy and household mortgage decisions. To this end, the longitudinal dataset for the US population from the Panel Study of Income Dynamics (PSID) was used. Evidence for links between financial literacy levels and (1) mortgage uptake, (2) mortgage interest rates, and (3) mortgage refinancing decisions were examined using the two waves (2015 and 2017) of PSID data, combined with the 2016 PSID supplementary questionnaire examining the measured financial literacy of household members. Our results revealed a positive link between financial literacy and mortgage possession and, additionally, between financial literacy and the subsequent decision to take out a mortgage. Moreover, higher financial literacy scores were associated with lower mortgage interests and a greater likelihood of mortgage refinancing. On average, a household that refinanced its mortgage was able to reduce its interest rate by almost 0.7 percentage points, providing evidence of the positive role of financial literacy in securing better mortgage terms.
Calder(cid:243)n(cid:146)s Type Reproducing Formula Related To The q -Dunkl Two Wavelet Theory (cid:3)

In this paper, using some elements of the q -harmonic analysis associated to the q -Dunkl operator introduced by N. Bettaibi et al. in [1], for (cid:133)xed 0 < q < 1 , the notion of a q -Dunkl two-wavelet is introduced. The resolution of the identity formula for the q -Dunkl continuous wavelet transform is then formulated and proved. Calder(cid:243)n(cid:146)s type reproducing formula in the context of the q -Dunkl two wavelet theory is proved.
Source materials for inception stage Hawaiian magmas: Pb‐He isotope variations for early Kilauea

New noble gas and radiogenic isotopic compositions are presented for tholeiitic, transitional, and alkalic rocks from the submarine Hilina region on the south flank of Kilauea, Hawaii. The 3He/4He ratios for undegassed glass and olivine separates (11–26 Ra) contrast with those of postshield and rejuvenated alkalic lavas, consistent with the alkalic and transitional basalts at Hilina corresponding to early Kilauea magmas. Most early Kilauea samples contain highly radiogenic Pb isotopes compared with other Hawaiian rocks and therefore derive from a Hawaiian plume end‐member source (here referred to as the Hilina component) distinctive in that respect. Besides radiogenic Pb isotopes, the Hilina component has relatively low 3He/4He (<12 Ra) among the Hawaiian magmas. Hawaiian inception stage magmas, including Hilina, Loihi, and deep Hana Ridge (east Maui), define a linear array in 206Pb/204Pb‐3He/4He isotope space, indicating that mixing between the Hilina and Loihi components (or their melts) dominates magmatism at the leading edge of the Hawaiian plume. The Hilina component's isotopic characteristics can be derived from young subduction‐recycled crust or metasomatised mantle. The isotopic differences between the geographically discriminated Kea and Loa trend volcanic chains, observed in shield stage lavas, are also seen in the inception stage magmas, suggesting that proportions of melts derived from the Hilina and Loihi components were different between the Kea and Loa trend volcanoes.
Cretaceous dinoflagellate provincialism in Brazilian marginal basins

Abstract Aptian to Maastrichtian dinoflagellate assemblages from northern and northeastern Brazilian basins define an Equatorial Atlantic Province, indicative of the Tethyan Realm. This contrasts with coeval assemblages from southern and southeastern Brazilian basins, which show Austral affinity and define a Tropical/Subtropical Atlantic Province. In the northeastern basins (Sao Luis, Potiguar, Araripe and Ceara) provincialism is marked by the Subtilisphaera Ecozone, which straddles the Aptian–Albian boundary. Diverse Albian dinoflagellate assemblages containing Gordiacysta coronata and Walvisia woodii , both previously reported only from South Atlantic basins, occur in southern and southeastern Brazilian basins (Pelotas, Santos and Campos basins). In northern and northeastern basins (offshore Para-Maranhao, Piaui, Ceara and Potiguar) there are no rich Albian dinoflagellate assemblages as a consequence of high terrigenous input. In the Cenomanian–Turonian of southern and southeastern Brazilian basins dinoflagellate assemblages are relatively poor, their low diversity being ascribed to anoxic oceanic events. However, in northern and northeastern basins assemblages are well represented and contain abundant specimens of the genera Circulodinium , Cyclonephelium and Florentinia . Some Florentinia species, e.g., F. berran and F. khaldunii , are typical of the Tethyan province. By contrast, these same species are absent in southern and southeastern basins. In the Senonian, provincialism is manifested mainly by differences among peridinioid dinoflagellates. Southern and southeastern basins contain Chatangiella , Nelsoniella , and Xenikoon . All three genera are rare in the northern and northeastern basins, which contain more diverse Cerodinium assemblages.
Ocean-Atmosphere Interaction and the Tropical Climatology. Part II: Why the Pacific Cold Tongue Is in the East.

Abstract The influence of coupled process on the climatology of the tropical Pacific is studied in a model for the interaction of equatorial SST, the associated component of the Walker circulation, and upper-ocean dynamics. In this part, the authors show how different physical mechanisms affect the spatial pattern of the Pacific warm pool and cold tongue in this coupled climatology. When model parameters give a suitable balance between effects of upwelling and thermocline depth on sea surface temperature and for suitable atmospheric parameters, a good prototype for the observed cold-tongue configuration is produced. This is largely determined by coupled ocean-atmosphere processes within the basin. Presence of an easterly wind s~ component produced by factors external to the Pacific basin can be important in setting up a cooling tendency, but this is magnified and modified by a chain of nonlinear feedbacks between trade winds and ocean dynamics affecting the SST gradient within the basin. These feedbacks d.
Inner core anisotropy in three dimensions

The purpose of this paper is the investigation of cylindrical anisotropy in the inner core based on the travel time anomalies of the PKIKP phase. We use the arrival times reported in the International Seismological Centre Bulletins for years 1964–1990. We select only earthquakes which have a good azimuthal coverage and a sufficiently large number of reporting stations. The earthquakes are relocated using corrections for lateral heterogeneity computed for our most recent three-dimensional mantle model. We use a total of 313,422 observations of the DF branch of PKP travel time anomalies within the epicentral distance ranges of 120°–140° and 150°–180° reported by 2335 stations for 26,377 earthquakes. We process the data using an averaging procedure, which we call cylindrical anisotropy stacking, that enhances the effects of anisotropy, but is expected to suppress those due to lateral heterogeneity and random errors. The processed residuals show a remarkably consistent pattern. This confirms the dominance of the cylindrical elastic anisotropy in the inner core with, approximately, a constant axis of symmetry. This axis of symmetry is found to be tilted 10.5°±1° from the Earth's rotation axis in the direction 160°E±5° in the northern hemisphere. In this new coordinate system we determine a four-layer axisymmetric model of transverse anisotropy with each layer approximately 300 km thick. The model shows that the anisotropy is strongest (>3%) within the innermost part of the core. The travel time anomalies show significant (±1.5 s) longitudinal variations, even when the tilt of the axis of symmetry is considered. There is a substantial increase in the amplitude of the longitudinal variations, which are dominated by the second and fourth harmonics, for rays with bottoming depths exceeding 400 km below the inner core boundary. The measurable tilt of the axis of symmetry and the presence of significant nonaxisymmetric signal may provide important clues with respect to the possible causes of anisotropy. The increase in the anisotropy in the innermost part of the core departs from earlier inferences that anisotropy may be limited to the outermost 200–300 km of the Earth's inner core.
Phytoplankton taxonomic variability in nutrient utilization and primary production in the Ross Sea

Patterns of nutrient utilization and primary productivity (PP) in late austral spring and early summer in the southwestern Ross Sea were characterized with respect to phytoplankton taxonomic composition, polynya dynamics, and upper ocean hydrography during the 1996–1997 oceanographic program Research on Ocean-Atmosphere Variability and Ecosystem Response in the Ross Sea. Phytoplankton biomass in the upper 150 m of the water column ranged from 40 to 540 mg chlorophyll a (Chl a) m−2, exceeding 200 mg Chl a m−2 everywhere except the extreme northern and eastern boundaries of the Ross Sea polynya. Diatom biomass was greatest in the shallow mixed layers of Terra Nova Bay, while the more deeply mixed waters of the Ross Sea polynya were dominated by Phaeocystis antarctica. Daily production computed from the disappearance of NO3 (1.14 g C m−2 d−1) and total dissolved inorganic carbon (TDIC, 1.29 g C m−2 d−1) is consistent with estimates made from an algorithm forced with satellite measurements of Chl a (1.25 g C m−2 d−1) and from measurements of 14C uptake (1.33 g C m−2 d−1). Phytoplankton PP in the Ross Sea averaged 100 g C m−2 yr−1 during 1996–1997. Despite the early formation of the Terra Nova Bay polynya the diatom bloom there did not reach its peak PP until middle to late January 1997 (most likely because of more intense wind mixing in November), ∼6 weeks after the P. antarctica bloom in the Ross Sea polynya had reached the same stage of development. From 70 to 100% of the C and N deficits in the upper 150 m could be accounted for by particulate organic matter, indicating that there had been little dissolved organic matter production or export of particulate material prior to our cruise. This suggests that early in the season, PP and zooplankton grazing are decoupled in the southwestern Ross Sea. The NO3∶PO4 disappearance ratio in waters dominated by P. antarctica (19.0±0.61) was significantly greater than in waters where diatoms were most common (9.52±0.33), and both were significantly different from the Redfield N∶P ratio of 16. Vertical profiles of TDIC suggest that P. antarctica took up 110% more CO2 per mole of PO4 removed than did diatoms, an important consideration for climate models that estimate C uptake from the removal of PO4.