1,802 research outputs found
Natural variation in Drosophila melanogaster
No full textThis work is dedicated to studying natural variation in D. melanogaster at the DNA sequence and gene expression level. In addition I present a new version of the DNA polymorphism analysis program VariScan, which includes significant improvements.
In CHAPTER 1 I describe a genome scan of single nucleotide polymorphism in two natural D. melanogaster populations (from Africa and Europe) on the third chromosome. Together with polymorphism data previously published for the X chromosome of the same populations, this allows a comparative study of the polymorphism patterns of the X chromosome and an autosome. The frequency spectrum of mutations and the patterns of linkage disequilibrium are investigated. The observed patterns indicate that there is a significant difference in the behavior of the two chromosomes, as has already been suggested by previous studies. To uncover the reasons for this a coalescent based maximum likelihood method is applied that incorporates the effects of demographic history and unequal sex ratios. For the African population the differential behavior of the chromosomes can be explained by its demographic history and an excess of females. In Europe, a population bottleneck and an excess of males alone cannot explain the patterns we observe. The additional action of positive selection in this population is proposed as a possible explanation.
In CHAPTER 2 I investigate the variation in gene expression of the two aforementioned populations. Whole-genome microarrays are used to study levels of expression for 88% of all known genes in eight adult males from both populations. The observed levels of expression variation are equal in Africa and Europe, despite the fact that DNA sequence variation is much higher in Africa. This is evidence for the action of stabilizing selection governing levels of expression polymorphism. Supporting this view, genes involved in many different functions, and are therefore on strong selective constraint, show less variation than do genes with only few functions. The experimental design allows the search for genes which differ in their expression patterns between Europe and Africa and might therefore have undergone adaptive evolution. Detected candidates include genes putatively involved in insecticide resistance and food choice. Surprisingly, many genes over-expressed in Africa are involved in the formation and function of the flying apparatus.
In CHAPTER 3 I present version 2 of the program VariScan. This program was designed to analyse patterns of DNA sequence polymorphism on a chromosomal scale. The functionality of the core analysis tool, the wavelet decomposition, is described. In addition, multiple improvements to the previous version are presented. The program now supports the “pairwise deletion” option. This is essential for analysing data at the chromosome scale, since such data often contains incomplete information. It is now possible to add outgroup information, which allows the calculation of additional statistics. Furthermore, the separate analysis of different predefined chromosomal regions is added as an option. To increase the user friendliness, a graphical user interface is now included as part of the software package. Finally, VariScan is applied to published and computer-generated data and the ability of the wavelet-based analysis to uncover chromosomal regions with interesting DNA polymorphism patterns is demonstrated
Deformation lines in Arctic sea ice: intersection angles distribution and mechanical properties - codes and intersection angle data
No full textCode and data to reproduce the results presented in Ringeisen et al. (2023). The included notebooks compute intersection angle distributions and distributions of deformation rates along LKFs, as well as derive yield curves from intersection angle distributions. The intersection angle data sets have been extracted from three different LKF datasets:
RGPS: Hutter, Nils (2019): Linear Kinematic Features (leads & pressure ridges) detected and tracked in sea-ice deformation simulated in an Arctic configuration of MITgcm using a 2-km horizontal grid spacing from 1997 to 2008. Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, PANGAEA, https://doi.org/10.1594/PANGAEA.909636
MOSAiC: Hutter, N. and von Albedyl, L. (in submission 2023): Linear Kinematic Features (leads & pressure ridges) detected and tracked in Sentinel-1 drift and deformation data during the MOSAiC expedition, PANGAEA
MITgcm simulations: Hutter, N. et al. (2022). Linear Kinematic Feature detected and tracked in sea-ice deformation simulationed by all models participating in the Sea Ice Rheology Experiment and from RGPS (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6315226
References: Ringeisen, D., Hutter, N., and von Albedyl, L. (2023). Deformation lines in Arctic sea ice: intersection angles distribution and mechanical properties. The Cryospher
Nymphargus lasgralarias Hutter & Guayasamin, new species
No full text<i>Nymphargus lasgralarias</i> Hutter & Guayasamin, new species <p>Figures 4 A–4C; 5B; 6A–6D; 7A–7D; 13D</p> <p> <b>Holotype.</b> MZUTI 0 96, adult male collected by Carl R. Hutter on 0 5 April 2011 from “Five Frog Creek” (0º01.870’ S, 78º42.358’ W; 2150 m) at Reserva Las Gralarias, Pichincha province, Ecuador. Figure 5 B.</p> <p> <b>Paratypes.</b> MZUTI 091–095, and 0 97, adult males obtained from Reserva Las Gralarias by Carl R. Hutter. MZUTI 093–095 were collected on 0 5 April 2011; MZUTI 0 92 on 17 April 2011; and MZUTI 0 91 on 18 April 2011 from “Kathy’s Creek” (0º01.398’ S, 78º43.772’ W; 2000 m). MZUTI 0 97 was collected on 0 1 July 2011 from “Hercules Giant Tree Frog Creek” (0º01.529’ S, 78º42.243’ W; 2175 m).</p> <p> <b>Generic placement.</b> All species in <i>Nymphargus</i> share an absence of webbing among Fingers I–III and absence or reduced webbing between Fingers III and IV. Additionally, males lack humeral spines (except <i>N. grandisonae</i>). The new species presents the aforementioned traits and, therefore, is placed in <i>Nymphargus</i> (<i>sensu</i> Guayasamin <i>et al.</i> 2009).</p> <p> <b>Diagnosis.</b> The new species can be distinguished from most species of <i>Nymphargus</i> by having a uniformly green dorsum (see Guayasamin <i>et al</i>. 2009). Within <i>Nymphargus</i>, the only species with a green dorsum that lacks spots are: <i>N. cristinae</i> (Ruiz-Carranza & Lynch 1995), <i>N. prasinus</i> (Duellman 1981), and <i>N. wileyi</i> (Guayasamin <i>et al.</i> 2006). <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> is distinguished from <i>N. cristinae</i> by being smaller (male SVL in <i>N. lasgralarias</i> = 24.6–26.5 mm [mean = 25.3 mm; <i>n</i> = 7]; male SVL in <i>N. cristinae</i> = 26.0– 31.1 mm [mean = 28.0 mm; <i>n</i> = 12]), having a snout that is truncate in dorsal view and protruding in lateral view (subacuminate in dorsal view, truncate in lateral view in <i>N. cristinae</i>; see Ruiz-Carranza & Lynch 1995: Fig. 4), lacking vomerine teeth (present or absent in <i>N. cristinae</i>), and lacking palmar supernumerary tubercles (supernumerary small, abundant in <i>N. cristinae</i>). <i>Nymphargus prasinus</i> differs from <i>N. lasgralarias</i> <b>sp. nov.</b> by having a round snout in dorsal view (truncate <i>N. lasgralarias</i> <b>sp. nov.</b>), 5–7 teeth on each process of the vomer (vomerine teeth absent in <i>N. lasgralarias</i> <b>sp. nov.</b>), and being considerably larger (male SVL 33.0– 34.5 mm; <i>n</i> = 3; see Duellman 1981). <i>Nymphargus wileyi</i> (an endemic of the Amazonian slopes of the Ecuadorian Andes) is distinguished from <i>N. lasgralarias</i> <b>sp. nov.</b> by having its kidneys covered by a white peritoneum with small, unpigmented spots (see Guayasamin <i>et al.</i> 2006: Fig. 12), whereas in the new species, the kidneys are covered by a homogenously white layer. Additionally, among <i>Nymphargus</i> species found on the Pacific versant of the Andes of Ecuador, <i>Nymphargus lasgralarias</i> <b>sp. nov</b>. could only be confused with <i>N. buenaventura</i> (Cisneros-Heredia & Yánez-Muñoz 2007) and <i>N. griffithsi</i> (Goin 1961). Dorsal texture and color pattern readily separates <i>N. buenaventura,</i> which, in life, has a light green dorsum with warts corresponding to pale yellow spots — whereas the dorsum of <i>N. lasgralarias</i> <b>sp. nov.</b> is shagreen (lacking warts) and homogenously green (lacking yellow spots). Additionally, <i>N. buenaventura</i> is smaller, although sample size is low (male SVL in <i>N. lasgralarias</i> <b>sp. nov.</b> = 24.6–26.5 mm [mean = 25.3 mm; <i>n</i> = 7]; male SVL in <i>N. buenaventura</i> = 20.9–22.4 mm [mean = 21.8; <i>n</i> = 4]). <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> and <i>N. buenaventura</i> are not known to occur sympatrically.</p> <p> <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> is most similar to <i>N. griffithsi</i>. However, the two species have differences in terms of dorsal color pattern (homogenously green with minute dark melanophores in <i>N. lasgralarias</i> <b>sp. nov.</b></p> <p> [Figs. 4 B, 6A–6B]); green with small black spots and/or both minute and small dark melanophores in <i>N. griffithsi</i> [Figs. 4 E, 6E–6F]), body size (male SVL in <i>N. lasgralarias</i> <b>sp. nov.</b> = 24.6–26.5 mm [mean = 25.3 mm; SD = 0.73 mm; <i>n</i> = 7]; male SVL in <i>N. griffithsi</i> = 22.5–24.2 mm [mean = 23.0 mm; SD = 0.70 mm; <i>n</i> = 5]; T-test: <i>p</i> <0.001), and call (see <i>Advertisement call</i> section). Additionally, in life, <i>N. griffithsi</i> has an iris background coloration of white-silver with larger and less abundant spotting with some medium-dark reticulation (Fig. 7 E–7H), whereas <i>N. lasgralarias</i> <b>sp. nov.</b> has a yellow-golden iris background color with lighter reticulation and more numerous, smaller spots (Fig. 7 A–7D).</p> <p> <b>Characterization.</b> (1) Vomerine teeth absent; (2) snout truncate in dorsal profile, protruding in lateral profile; (3) tympanum small; supratympanic fold present; tympanic membrane translucent, pigmented only on its upper half; (4) skin texture finely shagreen, with microspiculations; (5) ventral skin areolate, with pair of large, round warts on ventral surfaces of thighs below vent; cloaca surrounded by low warts, non-enameled; (6) upper half of ventral parietal peritoneum covered by iridophores (= white), all other peritonea translucent, except for thin layer of iridophores covering heart and renal capsules; (7) liver tetralobed; (8) humeral spines absent; (9) webbing absent between fingers; (10) foot about half webbed; webbing formula: I (2–2–) — (2+–2 1/2) II (2–2–) — (3– –3) III (2– –2) — (3– –3) IV (3–3+) — 2 V; (11) ulnar and tarsal folds low, barely evident, non-enameled; (12) nuptial pad Type I; prepollex not separated from Finger I; (13) first finger slightly shorter than second; (14) eye diameter larger that width of disc on Finger III; (15) in life, green dorsum, with minute dark melanophores; (16) in preservative, dorsum pale lavender; (17) iris golden-yellow, with numerous small black spots; weakly reticulated; (18) hands and feet yellowish green; melanophores absent from fingers and toes or, when present, restricted to dorsal surfaces of Finger IV and Toes IV and V; (19) males call from the upper side of leaves along streams; (20) calls emitted in series of 1–4 calls; each call sounding like a “tick” or “click”; pulsed; duration of 0.0160– 0.0440 s (mean = 0.0257 ± 0.0058; <i>n</i> = 119); call non-modulated to weakly modulated; dominant frequency at 3445.3–3962.2 Hz (mean = 3691.4 ± 131.9 Hz); (21) fighting behavior unknown; (22) egg clutches deposited on upper surface of leaves at terminal margin, transitioning to hanging as eggs develop; (23) tadpoles unknown; (24) SVL in adult males 24.6–26.5 mm (mean = 25.3 ± 0.737; <i>n</i> = 7); females unknown.</p> <p> <b>Description of holotype.</b> MZUTI 0 96, adult male, SVL 25.5 mm. Head wider than long; head length 32% SVL; snout truncate in dorsal profile, protruding in lateral view; canthus rostralis indistinct, straight; loreal region slightly concave; lips slightly flared; nostrils protuberant, closer to tip of snout than to eye, directed dorsolaterally; internarial area barely depressed. Eye large, directed anterolaterally at an angle of 45°; transverse diameter of disc of Finger III 57.6% eye diameter. Supratympanic fold conspicuous, obscuring dorsal portion of tympanic annulus; tympanum small (3% of SVL), oriented mostly vertically, but with slight posterolateral inclination; tympanic membrane transparent, partially pigmented and differentiated from surrounding skin. Dentigerous processes of vomer low, situated transversely between choanae, lacking teeth; choanae large, longitudinally rectangular; tongue ovoid, with ventral posterior third not attached to mouth floor and posterior margin notched; vocal slits extending posterolaterally from the lateral edge of tongue to angle of jaws. Humeral spine absent; ulnar fold low, barely evident, nonenameled; relative lengths of fingers: III> IV> II> I; webbing between fingers absent; discs expanded, nearly round; disc pads triangular; subarticular tubercles small, round, simple; few palmar supernumerary tubercles evident, low; palmar tubercle elliptical, simple; nuptial pad Type I (<i>sensu</i> Flores 1985), ovoid, granular, extending from ventrolateral base to dorsal surface of Finger I, covering the proximal half of Finger I. Length of tibia 56% SVL; low inner tarsal fold barely evident; outer tarsal fold absent; feet about half webbed; webbing formula of foot: <b>I</b> 2 – — 2 1/ 2 <b>II</b> 2– — 3 <b>III</b> 2– –– 3– <b>IV</b> 3— 2 <b>V</b>; discs on toes round; disc on Toe IV narrower that disc on Finger III; disc pads triangular; inner metatarsal tubercle large, ovoid; outer metatarsal tubercle round, barely evident; subarticular tubercles small, round; supernumerary tubercles absent.</p> <p>Skin on dorsal surfaces of head, body, and lateral surface of head and flanks shagreen with numerous minute spinules; throat smooth; belly and lower flanks areolate; cloacal opening directed posteriorly at upper level of thighs; cloacal warts small, fleshy, located immediately posterior to cloacal slit, non-enameled. Pair of large subcloacal tubercles evident in ventral aspect.</p> <p> <b>Measurements of holotype.</b> Morphometrics of the holotype and paratypes are summarized in Table 1.</p> <p> <i>Nymphargus lasgralarias</i> <b>sp. nov.</b></p> <p> <b>Color in life</b>. Dorsum light green, with minute melanophores; flanks yellowish white; bones green; fingers and toes yellow with a faint green tint. Venter white anteriorly and translucent posteriorly. Iris background golden with numerous dark spots and very light reticulation.</p> <p> <b>Color in preservative</b>. Dorsal surfaces of head and body are cream; fingers and toes cream. Upper half of ventral parietal peritoneum covered by iridophores (= white), all other peritonea translucent, except for thin layer of iridophores covering heart and renal capsules.</p> <p> <b>Variation</b>. In life, dorsal coloration varies from very light green to light green. Coloration of dorsum in preservation varies from cream to medium-dark lavender. Females are unknown.</p> <p> <b>Advertisement Call.</b> The call of <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> is reminiscent of a short “ticking” or “clicking” noise and is easily distinguishable from the significantly longer “whistle” produced by <i>Nymphargus griffithsi</i> (Figs. 8–10). The call consists of a short, pulsed note lasting 0.016– 0.044 s (mean = 0.026 ± 0.006 s) with 1–3 pulses (mean = 1.5 ± 0.6 pulses) (Figs. 9, 11 A–11C). Calls emitted in a series, which typically includes 1–4 calls (mean = 2.7 ± 0.7 calls) (Fig. 12 A–12D). Five-call series had been observed, but were not recorded. Each series has duration of 0.033– 2.541 s (mean = 1.529 ± 0.597 s) and an interval of 8.6– 78.6 s (mean 33.8 ± 18.4 s) between series with an interval of 0.088– 1.513 s (mean = 0.873 ± 0.205 s) between calls within a series. The call repetition rate is 2.0–9.9 (5.5 ± 2.7) calls per minute (<i>n</i> = 6 individuals). The dominant frequency is measured at 3445.3–3962.2 Hz (mean = 3691.4 ± 131.9 Hz); contained within the fundamental frequency. The individual call begins at an initial fundamental frequency of 2561.0–3441.0 Hz (mean 3063.6 ± 162.5 Hz). The fundamental frequency is bound between the lower frequency of 2939.4–4145.2 Hz (mean = 3236.3 ± 168.7) and the upper frequency of 3887.7–4473.4 Hz (mean = 4139.8 ± 139.7 Hz). The call has three harmonic frequencies at 6546.1– 8096.5 Hz (mean = 7298.9 ± 305.8 Hz), 9991.4–12058.6 Hz (mean = 11034.2 ± 478.3 Hz), and 13781.2–14928.0 Hz (mean 14317.1 ± 245.5 Hz).</p> <p> A quantitative comparison between the calls of <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> and <i>Nymphargus griffithsi</i> is shown in Table 2. Structurally, the calls of the two species are quite different (Fig. 8). The call of <i>N. griffithsi</i> is a single tonal or multi-pulsed (i.e., 2 or more pulses) call (Figs. 8 B, 10, 11D–11F), whereas the calls of <i>N. lasgralarias</i> <b>sp. nov.</b> are always pulsed (Figs. 8A, 9, 11 A–11C). <i>Nymphargus griffithsi</i> emits its advertisement call as a single call (absent from a series) while <i>N. lasgralarias</i> <b>sp. nov.</b> emits its calls as a single call or in a series, demonstrating a highly variable calling pattern in contrast to <i>N. griffithsi</i> (Fig. 12 A–12D). In addition, <i>N. lasgralarias</i> <b>sp. nov.</b> has a significantly shorter call duration than <i>N. griffithsi</i> (call duration in <i>N. lasgralarias</i> <b>sp. nov.</b> = 0.016– 0.044 s [mean = 0.026 s; SD = 0.006 s; <i>n</i> = 119]; call duration in <i>N. griffithsi</i> = 0.103– 0.148 s [mean = 0.122 s; SD = 0.009 s; <i>n</i> = 48]; T-test: <i>p</i> <0.001).</p> <p> The dominant frequency is significantly lower in <i>N. lasgralarias</i> <b>sp. nov.</b> than <i>N. griffithsi</i> (dominant frequency in <i>N. lasgralarias</i> <b>sp. nov.</b> = 3445.3–3962.2 Hz [mean = 3691.4 Hz; SD = 131.9 Hz; <i>n</i> = 119]; dominant frequency in <i>N. griffithsi</i> = 3789.8–4306.6 Hz [mean = 4107.4 Hz; SD = 105.5 Hz; <i>n</i> = 48]; T-test: <i>p</i> <0.001), although there is partial overlap. Although the calls of <i>N. lasgralarias</i> <b>sp. nov.</b> and <i>N. griffithsi</i> do not show a conspicuous change in dominant frequency, the two species show a slight increase in the dominant frequency, an increase that is more pronounced it <i>N. griffithsi</i>. Furthermore, <i>N. lasgralarias</i> <b>sp. nov.</b> has a significantly lower initialization frequency (Hz) than <i>N. griffithsi</i> (initial frequency in <i>N. lasgralarias</i> <b>sp. nov. =</b> 2561.0–3441.0 Hz [mean = 3063.6 Hz; SD = 162.5 Hz; <i>n</i> = 119]; initial frequency in <i>N. griffithsi</i> = 2821.0–3776.0 Hz [mean = 3328.6 Hz; SD = 300.9 Hz; <i>n</i> = 48]; T-test: <i>p</i> <0.001). A quantitative comparison between the calls of <i>N. lasgralarias</i> <b>sp. nov.</b> and <i>N. griffithsi</i> is shown in Table 2. Additional detailed acoustic measurements can be found in APPENDIX II and APPENDIX III.</p> <p> <b>Distribution.</b> <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> is known only from its type locality at Reserva Las Gralarias (Fig. 1) in Pichincha province, Ecuador, between an elevation of 1850–2200 m. Within the reserve, <i>N. lasgralarias</i> <b>sp. nov.</b> is known from the Chalguayacu Grande River (0º01.868’ S, 78º44.057’ W; 1925–2000 m), “Five Frog Creek”, “ Heloderma Creek” (0º01.245’ S, 78º42.370’ W; 2175–2225 m), “Hercules Giant Tree Frog Creek”, “Kathy’s Creek”, and “Lucy’s Creek” (0º00.585’ S, 78º43.901’ W; 1850–1875 m). <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> is quite ubiquitous throughout Reserva Las Gralarias, with observations only absent from the Santa Rosa River (0º01.192’ S, 78º43.212’ W; 1825–1850 m) (Table 3; Fig. 2).</p> <p> <b>Species</b></p> <p> <i>N. lasgralarias</i> <b>sp. nov.</b> <i>N. griffithsi</i></p> <p> Parameter Range Mean ± SD Range Mean ± SD <b>Species</b></p> <p> <i>Centrolene ballux Centrolene lynchi Centrolene peristictum Centrolene heloderma Nymphargus grandisonae Nymphargus griffithsi Nymphargus lasgralarias</i></p> <p>Ballux Creek</p> <p>(2150–2200 m) Five Frog Creek (2100– 2150 m)</p> <p>Heloderma Creek (2175–</p> <p>2225 m)</p> <p>Hercules Creek (2150–2200</p> <p>m)</p> <p>Chalguayacu River (1900–</p> <p>1950 m)</p> <p>Kathy´s Creek (1950–2050 m) Lucy´s Creek</p> <p>(1825–1875 m)</p> <p>Santa Rosa River (1800–</p> <p>1875 m)</p> <p> <b>Ecology and natural history.</b> <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> inhabits small sized permanent streams (ca. 3 m width) within primary montane forest with minimal disturbance. The species is active during the night and emits advertisement calls from the tops of small sized ferns, small leaves, and long palm leaves 1–6 m above the stream (Fig. 13 D). <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> occurs sympatrically with the following members of Centrolenidae: <i>Centrolene ballux, Centrolene heloderma,</i> <i>Centrolene lynchi</i> (Duellman 1980), <i>Centrolene peristictum</i> (Lynch & Duellman 1973), <i>Nymphargus grandisonae,</i> and <i>Nymphargus griffithsi</i> (Table 3). Other anuran species sympatric along the creeks include: <i>Hyloscirtus alytolylax</i> (Duellman 1972), <i>Pristimantis eugeniae</i> (Lynch & Duellman 1997), <i>Pristimantis calcarulatus</i> (Lynch 1976), <i>Pristimantis parvillus</i> (Lynch 1976), and <i>Pristimantis wnigrum</i> (Boettger 1892).</p> <p> Eggs are deposited on the tips of leaves over the stream and later expand into a hanging gelatinous mass upon absorption of water. We observed 12– 36 eggs per mass (mean = 25.4 ± 6.0 eggs; <i>n</i> = 23) for <i>N. lasgralarias</i> <b>sp. nov.</b> (Fig. 13 A–13B); we observed a single mass of <i>N. griffithsi</i> eggs containing 14 eggs (Fig. 13 C). The quantity of eggs per mass appears to be highly variable. The egg masses were distinguished by continual monitoring of calling male activity and observed close proximity of calling males. <i>Nymphargus lasgralarias</i> <b>sp. nov.</b> marks the third species of glassfrog in Ecuador with this egg habit type (i.e., eggs dangling from the tips of leaves) — after <i>N. griffithsi</i> and <i>N. wileyi</i> (Guayasamin <i>et al.</i> 2006).</p> <p> The Saloya River basin is the type locality for <i>N. griffithsi</i> (Goin 1961), a locality that is about 11 km from the population of <i>N. griffithsi</i> at Reserva Las Gralarias (Fig. 2). These populations are nearly connected through the regional river system — the Canchupi River and Saloya River both flow into the Mindo River connecting the two systems, with ca. a 1 km gap between the start of the Canchupi River and “Five Frog Creek”. It is unknown whether <i>N. griffithsi</i> and <i>N. lasgralarias</i> <b>sp. nov.</b> populations occur in between these two observed localities. At Reserva Las Gralari
Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps.
No full textWhere causal SNPs (single nucleotide polymorphisms) tend to accumulate within biological pathways, the incorporation of prior pathways information into a statistical model is expected to increase the power to detect true associations in a genetic association study. Most existing pathways-based methods rely on marginal SNP statistics and do not fully exploit the dependence patterns among SNPs within pathways.We use a sparse regression model, with SNPs grouped into pathways, to identify causal pathways associated with a quantitative trait. Notable features of our "pathways group lasso with adaptive weights" (P-GLAW) algorithm include the incorporation of all pathways in a single regression model, an adaptive pathway weighting procedure that accounts for factors biasing pathway selection, and the use of a bootstrap sampling procedure for the ranking of important pathways. P-GLAW takes account of the presence of overlapping pathways and uses a novel combination of techniques to optimise model estimation, making it fast to run, even on whole genome datasets.In a comparison study with an alternative pathways method based on univariate SNP statistics, our method demonstrates high sensitivity and specificity for the detection of important pathways, showing the greatest relative gains in performance where marginal SNP effect sizes are small
Aluminium Diffusion in copper layers
No full textEin Al-Cu-Schichtsystem wurde in Hinblick auf Diffusionsmechanismus und Diffusionskinetik untersucht. In-situ Heizversuche nach der -first arrival-- Methode wurden mit einem TOF-SIMS Gerät durchgeführt. Die Proben wurden auf einem beheizbaren Probenträger fixiert, auf die gewünschte Temperatur gebracht und dort so lange gehalten, bis das Al+- Signal an der Oberfläche zunahm. Nach einem einfachen mathematischen Modell von Crank1 wurden der Diffusionskoeffizient und die Aktivierungsenergie des Probensystems ohne Diffusionsbarriere bestimmt. Der Diffusionskoeffizient ist in der Größenordnung 10-14 m2/s und die Aktivierungsenergie EA wurde zu 0,64 eV bestimmt. Zur Evaluierung dieser einfachen Berechnungsmethode wurden die Daten aus der Doktorarbeit von R. Venos2, welche über AES und ein spezielles Modell für Korngrenzdiffusion bestimmt wurden, mit dem einfachen Ansatz nachgerechnet. Der Unterschied wird als vernachlässigbar gering angesehen. Es wurden Proben mit verschiedenem Schichtaufbau untersucht. Als Diffusionsbarriere dienten 50, 150 und 300 nm WTi, sowie 50 nm WTiN. Diese wurden unter den gleichen Bedingungen gemessen, wie die Proben ohne Barriere. Die Proben mit 150 und 300 nm WTi und mit 50 nm WTiN stellten sich als gute Barrieren heraus, welche die Diffusion bei 400 °C für mindestens 30 Minuten unterbinden. Für das Probensystem mit 50 nm ist diese Aussage nicht so einfach zu treffen. Die Messungen der Durchbruchzeit zeigen eine große Streuung. Daraus wurde geschlossen, dass die Diffusionsbarriere nicht dicht ist. Als Grund dafür kann die niedrige Schichtdicke angesehen werden. Ob es sich dabei um richtige Löcher handelt oder um dünne Stellen, welche eine Aluminiumdiffusion nicht ausreichend unterbinden, kann nicht gesagt werden. Ein Zusammenhang zwischen Barrierefehler und Durchbruchzeit konnte nicht gefunden werden. Die laterale Verteilung des Al+- Signals wurde untersucht. Während die Verteilung bei niedrigen Temperaturen relativ homogen ist, kann bei höheren Temperaturen eine Anreicherung an den Korngrenzen beobachtet werden. Auch die Verteilung unterhalb der Oberfläche kann auf die Korngrenzen bezogen werden, was beweist, dass Al über Korngrenzdiffusion an die Oberfläche kommt.An Al-Cu layer system was investigated with respect to diffusion mechanism and diffusion kinetics. In-situ heating measurements were performed with a TOF-SIMS instrument using the first arrival method. The samples were mounted to a heating stage and annealed at a certain temperature until the Al+ signal at the surface increased. After an easy mathematical equation by Crank1, the diffusion coefficient D is in the order of 10-14 m2/s and the activation energy is 0.64 eV for the sample system without diffusion barrier. For evaluation of the applied mathematical equations data from similar experiments with AES by R. Venos2 was compared. The more sophisticated model used there was compared with the easy approach that was applied in this work. The difference was found to be negligible. Samples with different diffusion barriers were also investigated. 50, 150 and 300 nm WTi and 50 nm WTiN served as barriers and were measured under the same conditions as the samples without diffusion barrier. The 150 and 300 nm WTi as well as the 50 nm WTiN were found to be suitable layers for preventing diffusion up to 400 °C for at least 30 min. For the sample with 50 nm no easy conclusion could be made. Measurements showed high scattering in arrival times. This was concluded to be a result of an imperfect diffusion barrier. As the barrier is really thin, it is supposed that holes and thinner regions can occur which are not able to withstand the diffusing Al. A connection between arrival times and barrier failures could not be found. The lateral distribution of the diffusing Al was investigated. Whereas the distribution is rather homogeneous at lower temperatures, enrichment along the grain boundaries on the surface is found at higher temperatures. Furthermore, the lateral distribution below the surface was investigated and it was found that Al reaches the surface via grain boundary diffusion
Merged grids of sea-ice or snow freeboard from helicopter-borne laser scanner during the MOSAiC expedition, version 1
No full textThis data set is a higher-processing-level version of Gridded segments of sea-ice or snow surface elevation and freeboard from helicopter-borne laser scanner during the MOSAiC expedition, version 1 (Hutter et al., 2022; doi:10.1594/PANGAEA.950339), where the individual 30-second segments of the small scale grid flights have been combined into merged grids. The data were collected using a near-infrared, line-scanning Riegl VQ-580 airborne laser scanner (https://hdl.handle.net/10013/sensor.7ebb63c3-dc3b-4f0f-9ca5-f1c6e5462a31 & https://hdl.handle.net/10013/sensor.7a931b33-72ca-46d0-b623-156836ac9550) mounted in a helicopter along the MOSAiC drift from the north of the Laptev Sea, across the central Arctic Ocean, and towards the Fram Strait from September 2019 to October 2020. The merged data are stored in netCDF and geotiff format. The data are drift corrected using the position and heading data of RV Polarstern and elevation offset corrected using overlapping segments to overcome degraded GPS altitude data >85°N. For the flights with degraded GPS altitude quality, we provide only a freeboard estimate. The merged grids include all data variables of the gridded 30-s segments: surface elevation, freeboard (estimate), freeboard uncertainty, estimated sea surface height, surface reflectance, echo width, and number of points used in the interpolation. Also the calculated elevation offset correction term is provided for each flight as a csv file
A fantastic new species of secretive forest frog discovered from forest fragments near Andasibe, Madagascar
No full textWe describe a fantastic new species of forest frog (Mantellidae: Gephyromantis: subgenus: Laurentomantis) from moderately high elevations in the vicinity of Andasibe, Madagascar. This region has been surveyed extensively and has a remarkably high anuran diversity with many undocumented species still being discovered. Surprisingly, by exploring areas around Andasibe that lacked biodiversity surveys, we discovered a spectacular and clearly morphologically distinct species, previously unknown to science, Gephyromantis marokoroko sp. nov., documented for the first time in 2015. The new species is well characterised by a very rugose and granular dorsum, dark brown skin with bright red mottling, sparse light orange to white spots on the ventre, vibrant red eyes and femoral glands present only in males that consist of eight medium-sized granules. Bioacoustically, the new species has a quiet advertisement call that differs from related species by having a moderate call duration, 2–4 strongly pulsed notes and a slow note repetition rate. Furthermore, it has substantial differentiation in mitochondrial DNA, with pairwise distances of 7–9% to all other related species in sequences of the mitochondrial 16S rRNA marker. Additional evidence is given through a combined four mitochondrial markers and four nuclear exons concatenated species tree, strongly supporting G. striatus as the sister species of the new species in both analyses. The discovery of this new species highlights the need for continued inventory work in high elevation rainforests of Madagascar, even in relatively well-studied regions © Copyright Carl R. Hutter et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]
Hyloscirtus princecharlesi Coloma & Carvajal-Endara & Dueñas & Paredes-Recalde & Morales-Mite & Almeida-Reinoso & Tapia & Hutter & Toral & Guayasamin 2012, sp. nov.
No full textHyloscirtus princecharlesi sp. nov. Figs. 1F, 11A, 12A–C Holotype. CJ 308 an adult male from a cascading stream on the border between Reserva Cotacachi-Cayapas and a private land owned by Manuel Quinchiguango, at Recinto San Antonio (ca. Cuellaje), Provincia Imbabura, Ecuador (0º 28' 23.772" N, 78º 34' 12.756" W; 2794 m); obtained on 22 July 2011 by Elicio E. Tapia, Carl R. Hutter, and Carlos Quinchiguango. Paratypes. QCAZ 43654, 44893 adult males with same locality as holotype (0º 28' 20.8194" N, 78º 33' 57.6" W; 2720–2794 m); the former obtained on 23 June 2009 by Elicio E. Tapia and William Quinchiguango, and the latter on 24 June 2009 by Luis A. Coloma, Manuel A. Morales-Mite, and Elicio E. Tapia. Diagnosis. A member of the Hyloscirtus larinopygion group as diagnosed by Faivovich et al. (2005). The new species differs from other members of that group by having a unique pattern of dorsal coloration (series of well defined orange blotches or spots densely and uniformly distributed on a black background), a genetic distance from other members of the group of at least 1.31% (for fragments of ~ 2.3 kb of aligned mitochondrial DNA sequences), poorly expanded digital discs, and a glandular nuptial pad on thumb. The most similar dorsal coloration is seen in H. pantostictus (Fig. 1E) and H. ptychodactylus (Fig. 1H), both of which have orange spots or blotches. Hyloscirtus princecharlesi differs from H. pantostictus from the slopes of northeastern Ecuador by having gray digital discs (yellow in H. pantostictus); also, the two species are not sister taxa (Fig. 3). The new species is distinguished from its sister species, H. ptychodactylus from the slopes of western Ecuador at Cotopaxi province by having well defined spots or blotches on dorsum (scattered, diffuse, spots or blotches and dense stipling among blotches in H. ptychodactylus), and by having a gray iris color (sky-blue in H. ptychodactylus). Description of holotype. SVL 70.5 mm. Body and limbs robust. Snout nearly truncate in dorsal and lateral view. Head about as broad as long. Head width at level of eyes (21.8 mm), 30.9% of SVL. Canthus rostralis rounded. Loreal region slightly concave. Lips rounded, not flared. Dorsal surface of internarial region nearly flat. Nostrils barely protuberant, directed anterolaterally, slightly posterior to anterior margin of lower jaw. Top of head nearly flat. Tympanum vertically ovoid, tympanic annulus distinct. Supratympanic fold thick, curved, covering dorsal edge of tympanum, extending from eye to posterior end of mandible and to shoulder. Forearms robust compared to upper arms. Axillary membrane absent. Ulnar tubercles absent. Fingers broad. Disks round, barely expanded or Finger I about same width as finger. Relative lengths of fingers 1<2<4<3. Lateral fringes absent. Palmar surface (Fig. 12B) with deep folds and low raised, round, supernumerary tubercles. Subarticular tubercles single, large, thick, rounded, or oval. Thenar tubercle thick, elliptical. Palmar tubercle barely noticeably. Prepollex absent. Glandular nuptial pad covering the outer margin of Finger I (Fig. 13A). Fingers webbed basally, manus webbing basal (Fig. 12B). Hind limb robust. Tibia length 46.5% of SVL. Heel tubercles absent. Inner tarsal fold absent. Foot length 44.7% of SVL. Inner metatarsal tubercle large, oval (Fig. 12C). Outer metatarsal tubercle absent. Subarticular tubercles round. Supernumerary, low raised tubercles present. Toe discs not expanded. Relative lengths of toes I<2<3<5<4. Foot webbing basal (Fig. 12C). Skin on throat and anterior portion of chest bearing irregular scattered folds on a weakly areolate skin that extends to abdomen. Pelvic patch areolate. Transverse supracloacal flap long. Margins of vent with numerous small folds and two large lateral swollen glandular areas at proximal posterior thighs. Cloacal opening directed posteriorly. Vocal slits present at posterior lingual margins of mandibles. Dentigerous processes of vomers long, transverse, abutting medially, behind level of large, ovoid choana, bearing 24 teeth evident in the buccal mucosa. Tongue broad, cordiform, shallowly notched posteriorly, fully attached to mouth floor, rugose on its anterior portion. Vocal sac single, median, subgular. Color in preservative (~70% ethanol). Dorsum with a pattern of dense, brown-orange, round-oval marks, and blotches on a black background, forming a reticulated pattern at mid-dorsum and more isolated blotches towards the flanks. Dorsum of limbs with larger marks and blotches than body. Anterior and posterior surfaces of thighs nearly black with two large faint gray blotches. Dorsum of inner fingers and toes gray with faint creamy-gray blotches that become brighter toward Fingers IV and Toes IV–V. Glandular area lateral to vent brown-orange. Throat, chest, abdomen with diffuse black-gray marbling. Inner margin of lower lip cream. Anterior flanks with three large round marks, posterior flanks barred. Tympanum mostly black. Color in life (Fig. 6B). Same as above except in that dorsal marks and blotches are orange, varying to pale orange. Blotches on hidden surfaces of thighs are creamy white. Ventral surfaces are black with yellow-cream marbling, more yellow at gular region. Tips of dorsal surfaces of fingers and toes are pale creamy-orange with gray. Palmar and plantar surfaces are gray to black. Ventral pads of digital discs on fingers and toes are gray. Iris is dark gray. Measurements of holotype (mm). SVL 70.5, TIBL 32.8, FEL 31.5, FOL 31.5, RDUL 17.9, HANDL 24.7, THBL 16.7, HLSQ 23.9, HDW 23.4, ITN 6.0, EYD 7.2, EYNO 4.7, TYD 3.6, DFW 3.9, DTW 3.1. Variation. Measurements variation of two paratypes (QCAZ 44893, 43654) and the holotype (CJ 308) are indicated in Table 7. The adult male paratypes overall are very similar to the holotype except for differences in color strength and patterns (Fig. 14), by bearing 29 vomerine teeth in QCAZ 44893 and 23 in QCAZ 43654, and by having slightly smaller finger discs in QCAZ 44893. Tadpoles. See under Tadpoles and ontogeny section. Distribution, natural history, and conservation status. Hyloscirtus princecharlesi is known only from its type locality (San Antonio, ca. border of Reserva Ecológica Cotacachi-Cayapas), a cascading stream in Montane Cloud Forest (Fig. 11C, D) (according to the classification proposed by Valencia et al. 1999). The locality is in northwestern Ecuador in the Cordillera de Toisán, a mountain range that is part of the Cordillera Occidental of the Ecuadorian Andes, in Provincia de Imbabura, at an elevation of 2720–2794 m (Fig. 9). At the type locality, the annual mean precipitation is 1671 mm and the annual mean temperature is 14.1 ºC (based on the WorldClim database; Hijmans et al. 2005). Toral et al. (2002) provide a detailed description of the type locality and a record of a female of this species (under the name Hyla sp 1.). The holotype CJ 308 was active during the night (21:50h) 2 m above the ground, on bushy vegetation, containing decomposing leaves mixed with mosses, and epiphytes, and surrounded by dense natural vegetation. It was located at the upper part of a cascade that was about 10 m wide and 8 m high. The headwater springs are about 20 m higher than the collecting site and about 80 m from the nearest divide. Paratypes QCAZ 44893 and 43654 were found active at 19:50h and 21:30h, respectively, at about the same site as the holotype. QCAZ 44893 was 1 m above ground on a leaf (approximately 30 x 40 cm) of an Anthurium sp., at the margin of a stream with natural vegetation. QCAZ 43654 was climbing on a branch 2 m above ground, close to a natural wall of stones, with abundant earth and epiphytic vegetation. There was no rain, the forest was cloudy. QCAZ 43654 was found at about 10 m from an individual of Hyloscirtus criptico . Hyloscirtus princecharlesi herein is considered as Endangered (A3ce IUCN criteria) due to a suspected population size reduction of ≥ 50% suspected to be met within the next 10 years, where the reduction or its causes may not have ceased. The single locality currently known for this species is being modified by human activities and is being severely affected by growing habitat destruction. Threats are logging, burning, unregulated use of land for agriculture, cattle raising, pesticide use, and invasive trout in the regional streams. Besides, it is likely that climate change and emerging pathogens are affecting its populations as has been documented for numerous other Andean frogs (Pounds et al. 2010). Rapid and integrative conservation measures are urgently needed, among which the protection and restoration of its habitat are a priority, as well as the establishment of an ex-situ assurance colony. Etymology. The specific name princecharlesi is a patronym that honors His Royal Highness Charles, Prince of Wales (Charles, Philip, Arthur, George, Windsor). In his call to halt tropical deforestation, Prince Charles uses frogs as symbols, and his Rainforests SOS Campaign includes a video with a frog as a rainforest ambassador. For this reason he is affectionately known by the media as the ‘frog prince’. Prince Charles is contributing significantly to the growth of awareness in the battle against tropical deforestation, climate change, and the catastrophic extinction of rainforest amphibians. His work is leading to increased awareness of these issues, and this increased awareness benefits biodiversity conservation, sustainability, alleviation of poverty, and ensures ecosystem services for present and future generations.Published as part of Coloma, Luis A., Carvajal-Endara, Sofía, Dueñas, Juan F., Paredes-Recalde, Arturo, Morales-Mite, Manuel, Almeida-Reinoso, Diego, Tapia, Elicio E., Hutter, Carl R., Toral, Eduardo & Guayasamin, Juan M., 2012, 3364, pp. 1-78 in Zootaxa 3364 on pages 26-3
Risk of colorectal cancer according to susceptibility SNPs in NHS, HPFS, PHS.
No full text<p>αWe used a surrogate rs2151512 for rs4925386 (linkage disequilibrium r<sup>2</sup> 1.0 in the HapMap CEU population).</p><p>βProximity to vitamin D response element (VDRE) based on published ChIP-seq data<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092212#pone.0092212-Ramagopalan1" target="_blank">[26]</a>.</p><p>χSNPs genotyped with TaqMan among 1895 CRC cases and 2806 controls.</p><p>δSNPs genotyped and imputed off Illumina HumanOmniExpress among 954 CRC cases and 1328 controls.</p><p>References: 1. Peters et al. Gastroenterology 2012; 2. Tenesa et al. Nature Genetics 2008; 3. Broderick et al. Nature Genetics 2007; 4. COGENT Nature Genetics 2008; 5. Tomlinson et al. Nature Genetics 2007; 6. Zanke et al. Nature Genetics 2007; 7. Haiman et al. Nature Genetics 2007; 8. Hutter et al. BMC Cancer 2010; 9. Tomlinson et al. Nature Genetics 2008; 10. Tomlinson et al. PLoS Genet, 2011; 11. Jaeger et al. Nature Genetics 2008; 12. Houlston et al. Nature Genetics 2010; 13. Jia et al. Nat Genet, 2012. 14. Dunlop et al. Nat Genet, 2012. 15. Kocarnik et al. CEBP, 2010. 16. Peters et al. Hum Genet, 2011.</p
Feature Reinforcement Learning : State of the Art
No full textAbstract Feature reinforcement learning was introduced five years ago as a principled and practical approach to history-based learning. This paper examines the progress since its inception. We now have both model-based and model-free cost functions, most recently extended to the function approximation setting. Our current work is geared towards playing ATARI games using imitation learning, where we use Feature RL as a feature selection method for high-dimensional domains. This paper is a brief summary of the progress so far in the Feature Reinforcement Learning framework (FRL) (Hutter 2009a), along with a small section on current research. FRL focuses on the general reinforcement learning problem where an agent interacts with an environment in cycles of action, observation-reward. The goal of the agent is to maximise an aggregation of the reward. The most traditional form of this general problem constrains the observations (and rewards) to be states which satisfy the Markov property, i.e. P (o t |o 1:t−1 ) = P (o t |o t−1 ) and is called a Markov Decision Process (MDP) Feature Reinforcement Learning (Hutter 2009a) is one way of dealing with the general RL problem, by reducing it to an MDP. It aims to construct a map from the history of an agent, which is its action-observation-reward cycles so far, to an MDP state. Traditional RL methods can then be used on the derived MDP to form a policy (a mapping from these states to actions). FRL fits in the category of a history-based approach. U-tree (McCallum 1996) is a different example of the history-based approach which uses a tree-based representation of the value function where nodes are split based on a local criterion. The cost in FRL is global, maps are accepted or rejected based on an evaluation of the whole map. While the idea behind FRL is simple, there are several choices to be made. What space do we draw the maps from, and how do we pick the one that fits our data so far? In the best case, we'd like to choose a map φ from the space of all possible (computable) functions on histories, but this is intractable in practice and the choice of a smaller hypothesis class can encode useful knowledge and improve learning speed. We define a cost-function that ideally measures how well φ maps the process to an MDP. The problem of searching through the map class for the best map φ * is addressed via a stochastic search method. Taking a step back from the history-based learning problem, we can frame the general RL problem as trying to find a map from a very-high dimensional input space, namely that of all possible histories to a policy representation that allows us to perform well in the given environment. This policy representation is often in the form of a value function but it does not have to be. The model-based feature RL framework Note that this representation of a general RL problem as a problem in a very-high dimensional input space allows us to use feature RL in the traditional learning setting for feature selection in function approximation problems. Instead of features of the history, our features are now that of the MDP state. The cost function now selects for the smallest subset of features that can represent our model or the valuefunction. Our current work is on using the value-based cost both in the off-policy and on-policy setting to deal with domains within the scope of the Arcade Learning Environment (Bellemare et al. 2013). The outline of this paper is as follows. Section 1 outlines some notation and relevant background, Section 2 deals with some related work, Section 3 looks at the Cost functions that have been examined in the FRL setting so far, and summarises the successes of the method. We conclude in Section 4. Preliminaries Agent-Environment Framework. The notation and framework is taken fro
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