1,368,294 research outputs found
High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland Moa (Megalapteryx didinus)
Full text linkKnowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand’s largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 14C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.Jamie R. Wood, Janet M. Wilmshurst, Steven J. Wagstaff, Trevor H. Worthy, Nicolas J. Rawlence and Alan Coope
MOA-2010-BLG-328Lb: a sub-Neptune orbiting very late M dwarf ?
Full text linkpeer reviewedWe analyze the planetary microlensing event MOA-2010-BLG-328. The best fit yields host and planetary masses of Mh = 0.11+/-0.01 M_{sun} and Mp = 9.2+/-2.2M_Earth, corresponding to a very late M dwarf and sub-Neptune-mass planet, respectively. The system lies at DL = 0.81 +/- 0.10 kpc with projected separation r = 0.92 +/- 0.16 AU. Because of the host's a-priori-unlikely close distance, as well as the unusual nature of the system, we consider the possibility that the microlens parallax signal, which determines the host mass and distance, is actually due to xallarap (source orbital motion) that is being misinterpreted as parallax. We show a result that favors the parallax solution, even given its close host distance. We show that future high-resolution astrometric measurements could decisively resolve the remaining ambiguity of these solutions
MOA-2010-BLG-311: A planetary candidate below the threshold of reliable detection
Full text linkpeer reviewedWe analyze MOA-2010-BLG-311, a high magnification (A_max>600) microlensing event with complete data coverage over the peak, making it very sensitive to planetary signals. We fit this event with both a point lens and a 2-body lens model and find that the 2-body lens model is a better fit but with only Delta chi^2~140. The preferred mass ratio between the lens star and its companion is $q=10^(-3.7+/-0.1), placing the candidate companion in the planetary regime. Despite the formal significance of the planet, we show that because of systematics in the data the evidence for a planetary companion to the lens is too tenuous to claim a secure detection. When combined with analyses of other high-magnification events, this event helps empirically define the threshold for reliable planet detection in high-magnification events, which remains an open question
Molecular and morphological analyses of avian eggshell excavated from a late thirteenth century earth oven
Full text linkUsing ancient DNA (aDNA) extracted from eggshell of the extinct moa (Aves: Dinornithiformes) we determined the species composition and number of eggs found in a late thirteenth century earth oven feature at Wairau Bar (South Island, New Zealand) - one of New Zealand's most significant archaeological sites. Mitochondrial and nuclear DNA signatures confirmed this oven feature contained fragments of at least 31 moa eggs, representing three moa genera: Emeus; Euryapteryx; Dinornis. We demonstrate through the genetic identification of 127 moa eggshell fragments that thickness is an unreliable character for species assignment. We also present a protocol for assessing the preservation likelihood of DNA in burnt eggshell. This is useful because eggshell fragments found in archaeological contexts have often been thermally modified, and heat significantly increases DNA fragmentation. Eggshell is widely used in radiocarbon dating and stable isotope research, this study showcases how aDNA can also add to our knowledge of eggshell in both archaeological and palaeoecological contexts
MOA-2011-BLG-262Lb : a sub-earth-mass moon orbiting a gas giant primary or a high velocity planetary system in the galactic bulge
Full text linkD.P.B. was supported by grants NASA-NNX12AF54G, JPL-RSA 1453175 and NSF AST-1211875. This MOA project is supported by the grants JSPS18253002 and JSPS20340052. T.S. acknowledges the financial support from the JSPS, JSPS23340044, JSPS24253004. This work was partially supported by a NASA Keck PI Data Award, administered by the NASA Exoplanet Science Institute. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. B.S.G. and A.G. were supported by NSF grant AST 110347. B.S.G., A.G., R.P.G. were supported by NASA grant NNX12AB99G. S.D. was partly supported through a Ralph E. and Doris M. Hansmann Membership at the IAS and by NSF grant AST-0807444. Work by J.C.Y. was performed in part under contract with the California Institute of Technology (Caltech) funded by NASA through the Sagan Fellowship Program. The OGLE project has received funding from the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement No. 246678 to A.U. D.H. was supported by Czech Science Foundation grant GACR P209/10/1318. D.M.B., M.D., K.H., C.S., R.A.S., M.H. and Y.T. are supported by NPRP grant NPRP-09-476-1-78 from the Qatar National Research Fund (a member of the Qatar Foundation).We present the first microlensing candidate for a free-floating exoplanet-exomoon system, MOA-2011-BLG-262, with a primary lens mass of M host ~ 4 Jupiter masses hosting a sub-Earth mass moon. The argument for an exomoon hinges on the system being relatively close to the Sun. The data constrain the product MLπrel where ML is the lens system mass and πrel is the lens-source relative parallax. If the lens system is nearby (large πrel), then ML is small (a few Jupiter masses) and the companion is a sub-Earth-mass exomoon. The best-fit solution has a large lens-source relative proper motion, μrel = 19.6 ± 1.6 mas yr–1, which would rule out a distant lens system unless the source star has an unusually high proper motion. However, data from the OGLE collaboration nearly rule out a high source proper motion, so the exoplanet+exomoon model is the favored interpretation for the best fit model. However, there is an alternate solution that has a lower proper motion and fits the data almost as well. This solution is compatible with a distant (so stellar) host. A Bayesian analysis does not favor the exoplanet+exomoon interpretation, so Occam's razor favors a lens system in the bulge with host and companion masses of M host = 0.12 +0.19-0.06 MΘ and mcomp = 18+28-10M⊕, at a projected separation of a⊥ = 0.84+0.25−0.14 AU. The existence of this degeneracy is an unlucky accident, so current microlensing experiments are in principle sensitive to exomoons. In some circumstances, it will be possible to definitively establish the mass of such lens systems through the microlensing parallax effect. Future experiments will be sensitive to less extreme exomoons.Peer reviewe
Interpretation of a short-term anomaly in the gravitational microlensing event MOA-2012-BLG-486
Full text linkD.M.B., M.D., K.H., M.H., S.I., C.S., R.A.S., and Y.T. are supported by NPRP grant NPRP-09-476-1-78 from the Qatar National Research Fund (a member of Qatar Foundation). K.H. is supported by a Royal Society Leverhulme Senior Research Fellowship.A planetary microlensing signal is generally characterized by a short-term perturbation to the standard single lensing light curve. A subset of binary-source events can produce perturbations that mimic planetary signals, thereby introducing an ambiguity between the planetary and binary-source interpretations. In this paper, we present the analysis of the microlensing event MOA-2012-BLG-486, for which the light curve exhibits a short-lived perturbation. Routine modeling not considering data taken in different passbands yields a best-fit planetary model that is slightly preferred over the best-fit binary-source model. However, when allowed for a change in the color during the perturbation, we find that the binary-source model yields a significantly better fit and thus the degeneracy is clearly resolved. This event not only signifies the importance of considering various interpretations of short-term anomalies, but also demonstrates the importance of multi-band data for checking the possibility of false-positive planetary signals.Peer reviewe
MOA-seq identifies shared and unique regions in open chromatin.
No full textComparison of MOA-seq to open chromatin profiling techniques DNS-Seq and ATAC-Seq. (A) Genome-wide distribution of MOA-seq footprints relative to genomic annotations. (B) MOA-seq read coverage (CPM) is non-randomly distributed around genes. Genes were scaled (metagene) to 2kb and average coverage is shown within the metagene body and adjacent genomic regions +/- 1.5kb from the nearest metagene boundary (grey dash). (C) Comparative analysis, shown as bar graphs, of MOA-seq peaks overlapping (shared, blue, %) or non-overlapping (unique, yellow) with ATAC-seq (MOA/ATAC), and the reciprocal intersections (ATAC/MOA). (D) and (E) Distribution of previously published DNS-seq (Positive light-heavy digest = blue, negative = red), ATAC-Seq (grey) coverage, MOA-seq (light orange) coverage (Mc) and peaks (Mp), and MF (dark orange) coverage (Mfc) and peaks (Mfp), surrounding example genes, vp14 (D) and dwf4/brs1 (E), with direction of transcription and the TSS indicated (arrow).</p
Profiling the dead: generating microsatellite data from fossil bones of extinct Megafauna — protocols, problems, and prospects
Full text linkWe present the first set of microsatellite markers developed exclusively for an extinct taxon. Microsatellite data have been analysed in thousands of genetic studies on extant species but the technology can be problematic when applied to low copy number (LCN) DNA. It is therefore rarely used on substrates more than a few decades old. Now, with the primers and protocols presented here, microsatellite markers are available to study the extinct New Zealand moa (Aves: Dinornithiformes) and, as with single nucleotide polymorphism (SNP) technology, the markers represent a means by which the field of ancient DNA can (preservation allowing) move on from its reliance on mitochondrial DNA. Candidate markers were identified using high throughput sequencing technology (GS-FLX) on DNA extracted from fossil moa bone and eggshell. From the ‘shotgun’ reads, >60 primer pairs were designed and tested on DNA from bones of the South Island giant moa (Dinornis robustus). Six polymorphic loci were characterised and used to assess measures of genetic diversity. Because of low template numbers, typical of ancient DNA, allelic dropout was observed in 36–70% of the PCR reactions at each microsatellite marker. However, a comprehensive survey of allelic dropout, combined with supporting quantitative PCR data, allowed us to establish a set of criteria that maximised data fidelity. Finally, we demonstrated the viability of the primers and the protocols, by compiling a full Dinornis microsatellite dataset representing fossils of c. 600–5000 years of age. A multi-locus genotype was obtained from 74 individuals (84% success rate), and the data showed no signs of being compromised by allelic dropout. The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research
MOA-seq read coverage and genome-wide distribution compared to DNS-seq.
No full text(A) Browser screenshot from a 100 kb region around the maize tb1 gene showing congruence of MOA-seq profiles with those of open chromatin from DNS-seq [7]. Browser tracks show "Clean Repeats excluding dust," from plants.ensembl.org (repeats), conserved non-coding sequences, CNS_ZL_v319c (CNS), gene models from Ensembl/Gramene (genes), earshoot iSeg peaks called at stringency bc2.0 (ES DNS iSeg bc2.0), earshoot differential nuclease sensitivity (ES DNS) profiles with positive/blue MNase-sensitive regions and negative/red MNase-resistant regions, earshoot MOA-seq coverage for 1-2mm earshoots (ES MOA (B) cov, S5 File) and associated iSeg peaks at four stringences (ES MOA (B) iSeg bc1,3,5, & 7), earshoot MOA-seq coverage for 0.5-5cm earshoots (ES MOA (A-D) cov) and associated iSeg peaks at four stringences (ES MOA (A-D) iSeg bc1,3,5, & 7), and DNS profiles for coleoptile node (CN), root tip (RT), and 15 day endosperm (EN). The combined MOA-seq coverage data and peaks called at iSeg bc5 used for subsequent analysis are highlighted (boxes & arrows). (B) 7 kbp zoom of the region ~ 60 kb upstream of tb1 showing substructure (arrows) of MOA-seq relative to open chromatin mapped by DNS-seq. (C) Bar chart showing % overlap of combined ES-MOA peaks at iSeg-bc5 with DNS-seq positive peaks at iSeg-bc2 for tissues indicated below the graph. (D) Bar chart showing % overlap of ES DNS-seq positive peaks with the three other DNS-seq tissues using iSeg-bc2 for all comparisons. (EPS)</p
Soft-tissue specimens from pre-European extinct birds of New Zealand
No full textWe provide the first complete review of soft tissue remains from New Zealand birds that became extinct prior to European settlement (c. AD 1800). These rare specimens allow insights into the anatomy and appearance of the birds that are not attainable from bones. Our review includes previously unpublished records of ‘lost’ specimens, and descriptions of recently discovered specimens such as the first evidence of soft tissues from the South Island goose (Cnemiornis calcitrans). Overall, the soft tissue remains are dominated by moa (with specimens from each of the six genera), but also include specimens from Finsch's duck (Chenonetta finschi) and the New Zealand owlet-nightjar (Aegotheles novaezealandiae). All desiccated soft tissue specimens that have radiocarbon or stratigraphic dates are late Holocene in age, and most have been found in the semi-arid region of Central Otago
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