DNA from extinct giant lemurs links archaeolemurids to extant indriids

<p>Abstract</p> <p>Background</p> <p>Although today 15% of living primates are endemic to Madagascar, their diversity was even greater in the recent past since dozens of extinct species have been recovered from Holocene excavation sites. Among them were the so-called "giant lemurs" some of which weighed up to 160 kg. Although extensively studied, the phylogenetic relationships between extinct and extant lemurs are still difficult to decipher, mainly due to morphological specializations that reflect ecology more than phylogeny, resulting in rampant homoplasy.</p> <p>Results</p> <p>Ancient DNA recovered from subfossils recently supported a sister relationship between giant "sloth" lemurs and extant indriids and helped to revise the phylogenetic position of <it>Megaladapis edwardsi </it>among lemuriformes, but several taxa – such as the Archaeolemuridae – still await analysis. We therefore used ancient DNA technology to address the phylogenetic status of the two archaeolemurid genera (<it>Archaeolemur </it>and <it>Hadropithecus</it>). Despite poor DNA preservation conditions in subtropical environments, we managed to recover 94- to 539-bp sequences for two mitochondrial genes among 5 subfossil samples.</p> <p>Conclusion</p> <p>This new sequence information provides evidence for the proximity of <it>Archaeolemur </it>and <it>Hadropithecus </it>to extant indriids, in agreement with earlier assessments of their taxonomic status (Primates, Indrioidea) and in contrast to recent suggestions of a closer relationship to the Lemuridae made on the basis of analyses of dental developmental and postcranial characters. These data provide new insights into the evolution of the locomotor apparatus among lemurids and indriids.</p

Multi-instrument analysis of 67P/Churyumov-Gerasimenko coma particles: COPS-GIADA data fusion

The European Space Agency's Rosetta mission to comet 67P/Churyumov-Gerasimenko has offered scientists the opportunity to study a comet in unprecedented detail. Four instruments of the Rosetta orbiter, namely, the Micro-Imaging Dust Analysis System (MIDAS), the Grain Impact Analyzer and Dust Accumulator (GIADA), the COmetary Secondary Ion Mass Analyser (COSIMA), and the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) have provided information on cometary dust particles. Cross-instrument comparisons are crucial to characterize cometary dust particles beyond the capabilities of individual sensors, as they are sensitive to different dust components. We present the first comparison between detections of the ROSINA COmet Pressure Sensor (COPS) and GIADA. These two instruments are complementary as the former is sensitive solely to volatiles of icy particles, while the latter measured the dust particle as a whole, including refractories and condensed (semi)volatiles. Our goal is to correlate the particles detected by COPS and GIADA and to assess whether they belong to a common group. We statistically analyzed the in situ data of COPS and GIADA by calculating Pearson correlation coefficients. Among the several types of particles detected by GIADA, we find that COPS particles are significantly correlated solely with GIADA fluffy agglomerates (Pearson correlation coefficient of 0.55 and p-value of $4.6\cdot 10^{-3}$). This suggests that fluffy particles are composed of both refractories and volatiles. COPS volatile volumes, which may be represented by equivalent spheres with a diameter in the range between 0.06 $\mu$m and 0.8 $\mu$m, are similar to the sizes of the fractal particle's subunits identified by MIDAS (i.e., 0.05-0.18 $\mu$m).Comment: 6 pages, 3 figures, accepted for publication in A&

A prototype liquid Argon Time Projection Chamber for the study of UV laser multi-photonic ionization

This paper describes the design, realization and operation of a prototype liquid Argon Time Projection Chamber (LAr TPC) detector dedicated to the development of a novel online monitoring and calibration system exploiting UV laser beams. In particular, the system is intended to measure the lifetime of the primary ionization in LAr, in turn related to the LAr purity level. This technique could be exploited by present and next generation large mass LAr TPCs for which monitoring of the performance and calibration plays an important role. Results from the first measurements are presented together with some considerations and outlook.Comment: 26 pages, 27 figure

Volatiles in the H2_2O and CO2_2 ices of comet 67P/Churyumov-Gerasimenko

ESA's Rosetta spacecraft at comet 67P/Churyumov-Gerasimenko (67P) was the first mission that accompanied a comet over a substantial fraction of its orbit. On board was the ROSINA mass spectrometer suite to measure the local densities of the volatile species sublimating from the ices inside the comet's nucleus. Understanding the nature of these ices was a key goal of Rosetta. We analyzed the primary cometary molecules at 67P, namely H$_2$O and CO$_2$, together with a suite of minor species for almost the entire mission. Our investigation reveals that the local abundances of highly volatile species, such as CH$_4$ and CO, are reproduced by a linear combination of both H$_2$O and CO$_2$ densities. These findings bear similarities to laboratory-based temperature programmed desorption experiments of amorphous ices and imply that highly volatile species are trapped in H$_2$O and CO$_2$ ices. Our results do not show the presence of ices dominated by these highly volatile molecules. Most likely, they were lost due to thermal processing of 67P's interior prior to its deflection to the inner solar system. Deviations in the proportions co-released with H$_2$O and CO$_2$ can only be observed before the inbound equinox, when the comet was still far from the sun and the abundance of highly volatile molecules associated with CO$_2$ outgassing were lower. The corresponding CO$_2$ is likely seasonal frost, which sublimated and lost its trapped highly volatile species before re-freezing during the previous apparition. CO, on the other hand, was elevated during the same time and requires further investigation.Comment: This is a pre-copyedited, author-produced PDF of an article accepted for publication in Monthly Notices of the Royal Astronomical Society following peer review. The version of record is available online at: https://doi.org/10.1093/mnras/stad300

Volatiles in the H2O and CO2 ices of comet 67P/Churyumov–Gerasimenko

European Space Agency’s Rosetta spacecraft at comet 67P/Churyumov–Gerasimenko (67P) was the first mission that accompanied a comet over a substantial fraction of its orbit. On board was the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis mass spectrometer suite to measure the local densities of the volatile species sublimating from the ices inside the comet’s nucleus. Understanding the nature of these ices was a key goal of Rosetta. We analysed the primary cometary molecules at 67P, namely H2O and CO2, together with a suite of minor species for almost the entire mission. Our investigation reveals that the local abundances of highly volatile species, such as CH4 and CO, are reproduced by a linear combination of both H2O and CO2 densities. These findings bear similarities to laboratory-based temperature-programmed desorption experiments of amorphous ices and imply that highly volatile species are trapped in H2O and CO2 ices. Our results do not show the presence of ices dominated by these highly volatile molecules. Most likely, they were lost due to thermal processing of 67P’s interior prior to its deflection to the inner solar system. Deviations in the proportions co-released with H2O and CO2 can only be observed before the inbound equinox, when the comet was still far from the sun and the abundance of highly volatile molecules associated with CO2 outgassing were lower. The corresponding CO2 is likely seasonal frost, which sublimated and lost its trapped highly volatile species before re-freezing during the previous apparition. CO, on the other hand, was elevated during the same time and requires further investigation

DNA Fingerprinting of Pearls to Determine Their Origins

We report the first successful extraction of oyster DNA from a pearl and use it to identify the source oyster species for the three major pearl-producing oyster species Pinctada margaritifera, P. maxima and P. radiata. Both mitochondrial and nuclear gene fragments could be PCR-amplified and sequenced. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in the internal transcribed spacer (ITS) region was developed and used to identify 18 pearls of unknown origin. A micro-drilling technique was developed to obtain small amounts of DNA while maintaining the commercial value of the pearls. This DNA fingerprinting method could be used to document the source of historic pearls and will provide more transparency for traders and consumers within the pearl industry

A Proposal for a Three Detector Short-Baseline Neutrino Oscillation Program in the Fermilab Booster Neutrino Beam

A Short-Baseline Neutrino (SBN) physics program of three LAr-TPC detectors located along the Booster Neutrino Beam (BNB) at Fermilab is presented. This new SBN Program will deliver a rich and compelling physics opportunity, including the ability to resolve a class of experimental anomalies in neutrino physics and to perform the most sensitive search to date for sterile neutrinos at the eV mass-scale through both appearance and disappearance oscillation channels. Using data sets of 6.6e20 protons on target (P.O.T.) in the LAr1-ND and ICARUS T600 detectors plus 13.2e20 P.O.T. in the MicroBooNE detector, we estimate that a search for muon neutrino to electron neutrino appearance can be performed with ~5 sigma sensitivity for the LSND allowed (99% C.L.) parameter region. In this proposal for the SBN Program, we describe the physics analysis, the conceptual design of the LAr1-ND detector, the design and refurbishment of the T600 detector, the necessary infrastructure required to execute the program, and a possible reconfiguration of the BNB target and horn system to improve its performance for oscillation searches.Comment: 209 pages, 129 figure

Cometary dust analogues for physics experiments

The CoPhyLab (Cometary Physics Laboratory) project is designed to study the physics of comets through a series of earth-based experiments. For these experiments, a dust analogue was created with physical properties comparable to those of the non-volatile dust found on comets. This "CoPhyLab dust" is planned to be mixed with water and CO$_2$ ice and placed under cometary conditions in vacuum chambers to study the physical processes taking place on the nuclei of comets. In order to develop this dust analogue, we mixed two components representative for the non-volatile materials present in cometary nuclei. We chose silica dust as representative for the mineral phase and charcoal for the organic phase, which also acts as a darkening agent. In this paper, we provide an overview of known cometary analogues before presenting measurements of eight physical properties of different mixtures of the two materials and a comparison of these measurements with known cometary values. The physical properties of interest are: particle size, density, gas permeability, spectrophotometry, mechanical, thermal and electrical properties. We found that the analogue dust that matches the highest number of physical properties of cometary materials consists of a mixture of either 60\%/40\% or 70\%/30\% of silica dust/charcoal by mass. These best-fit dust analogue will be used in future CoPhyLab experiments

Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters!

BACKGROUND:New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. METHODOLOGY/PRINCIPAL FINDINGS:We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)). CONCLUSIONS/SIGNIFICANCE:Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically considering heterochroneous models when analyzing heterochroneous samples covering a large time scale

The Microcephalin Ancestral Allele in a Neanderthal Individual

Background: The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans.1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings: Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH