Lower Ne Research Articles

PCN108 AN ECONOMIC MODEL TO ESTIMATE THE COST OF CYTOKINE RELEASE SYNDROME (CRS) AND NEUROLOGIC EVENTS (NE) OBSERVED IN CHIMERIC ANTIGEN RECEPTOR (CAR) T-CELL THERAPIES ADMINISTERED TO PATIENTS WITH RELAPSED/REFRACTORY (R/R) LARGE B-CELL LYMPHOMA (LBCL)

To estimate mean patient costs of CRS and NE for R/R LBCL population treated in the third-line or later with CAR T-cell therapy (lisocabtagene maraleucel [liso-cel], axicabtagene ciloleucel [axi-cel], and tisagenlecleucel). This economic model estimated 2019 provider costs using CRS and NE rates from clinical trials; CRS and NE management costs were estimated from a liso-cel study (Abramson, ASCO 2019; Yescarta PI; Kymriah PI). Grade 1–2 CRS was 40%, 81%, and 51%; grade 3–4 CRS was 2%, 13%, and 23% with liso-cel, axi-cel, and tisagenlecleucel, respectively (Lee criteria were used for liso-cel and axi-cel; Penn criteria were used for tisagenlecleucel). Grade 1–2 NE was 20%, 56%, and 40%; grade 3–4 NE was 10%, 31%, and 18% with liso-cel, axi-cel, and tisagenlecleucel, respectively. Means and 95% confidence intervals (CI) for types/grades of CRS and NE were estimated using Monte Carlo simulation (1000 runs). Assumptions were made regarding data inputs. Mean (95% CI) per-patient costs for all-grade CRS and NE were $16,347 ($15,988–$17,482), $50,088 ($49,053–$53,570), and $43,334 ($42,403–$46,344) for liso-cel, axi-cel, and tisagenlecleucel, respectively. Mean (95% CI) per-patient costs were $7715 ($7540–$8251), $23,309 ($22,817–$24,928), and $27,550 ($26,974–$29,465) for CRS with liso-cel, axi-cel, and tisagenlecleucel, respectively, and $8632 ($8447–$9231), $26,779 ($26,236–$28,641), and $15,784 ($15,429–$16,879), respectively, for NE. For an institution treating 100 patients with R/R LBCL with a CAR T-cell therapy cost of $373,000, the opportunity gain of using liso-cel could result in the ability to treat an additional 9.0 and 7.2 patients versus axi-cel and tisagenlecleucel, respectively. Potential cost offsets for liso-cel due to lower CRS and NE rates were $33,741 and $26,987, versus axi-cel and tisagenlecleucel, respectively, showing that differences in safety profiles among CAR T-cell therapies are economically important.

Separating divertor closure effects on divertor detachment and pedestal shape in DIII-D

Comparison between an open divertor and a more-closed divertor in DIII-D demonstrates detachment up to 40% lower pedestal density (ne,ped) in the closed divertor due to a combination of decreased fueling of the pedestal and increased dissipation in the scrape off layer (SOL) in the closed divertor, both resulting from increased neutral trapping in the divertor. Predicting whether the relationship between divertor closure and detachment will hold for an opaque SOL, in which the contribution of ionizing neutrals to fueling the pedestal is lessened, requires separating out different mechanisms contributing to the density difference at detachment. A series of experiments on DIII-D characterizes matched discharges using various divertor configurations to isolate the effects of divertor closure. These experiments show detachment up to 25% lower ne,sep in the closed divertor than in the open divertor, supported by simulations showing increased neutral trapping, and hence, increased dissipation, in the closed divertor. A difference in ne,ped/ne,sep is also seen: for matched ne,sep, the closed divertor has up to 20% lower ne,ped, consistent with modeling showing a smaller ionization fraction inside the separatrix in this case. Understanding how these pieces fit together will help in the development of predictive models of pedestal density and detached divertors compatible with a high performance core.

The breeding structure for the small ruminant resources in India.

Intense selection for a few desired traits has resulted in reduction of the effective population size (Ne) in most of the plant and livestock populations across the world. The objective of the research was to assess the impact of Ne on the genetic architecture of the population in a simulated data with variable Ne for general population under selection. Along with this, the estimate of Ne and its ratio to adult breeding population (NB) in the census data of small ruminants of India were also investigated. Results indicated that the average inbreeding ([Formula: see text]) decreases with increase in Ne; similarly, increase in [Formula: see text] per generation was highest in population with lowest Ne. Correlation of estimated breeding value (EBV) with true breeding value (TBV) was not much affected with effective population size. An effective number of chromosome segments (Me) in the populations under selection were significantly affected by magnitude of Ne, with linear positive relation between Ne and Me. Results on livestock census data revealed that all the sheep and goat breeds have sufficiently large Ne based on derived and actual census data. The median for ratio of effective population size to adult census size insheep breeds was 0.120 and for goat breeds was 0.131. Karnah and Poonchi sheep shares the status of endangered breeds due to a smaller number of breeding female population and hence need attention for conservation. The Ne was large in sheep and goat due to less selection pressure as a result of low coverage of breed improvement programs, availability of large number of breeding males, and absence of artificial insemination (AI) in the field flocks. The estimates of Ne and its ratio to the adult census size (NB) excluded several factors such as fluctuating population size and overlapping generations. Study revealed introspection from most of the industrial breeding programs on the issue of Ne for populations under selection. Similarly, in small ruminants, large Ne indicates huge genetic diversity and scope of improvement in the productivity in near future.

Dependence of Photovoltaic Properties of Spray-Pyrolyzed F-Doped SnO2 Thin Film on Spray Solution Preparation Method

Spray pyrolysis deposition of SnCl2.2H2O- and NH4F-containing solution is an appropriate method for deposition of fluorine-doped tin oxide (FTO), which has extensive applications in photovoltaic devices. According to a literature review, several spray preparation methods have been studied. These methods lead to both precipitated and unprecipitated spray solutions. Precipitated and unprecipitated solutions were used for deposition of FTO thin films. FTO obtained from unprecipitated solution yielded the lowest sheet resistance and resistivity, which was due to its highest electron concentration (ne). However, precipitation had no influence on electron mobility. The x-ray diffraction patterns of precipitates showed the presence of Sn- and F-containing compounds, which implied partial depletion of F and Sn from solutions. As a result, a lower amount of F− ions was incorporated into FTO, which led to lower ne. In addition, partial depletion of Sn led to slightly smaller FTO thickness. Finally, FTO thin film deposited from unprecipitated solution gave the highest figure of merit. This means that precipitation in the precursor solution has deleterious effects on electrical and optical properties.

123 Growth performance and nutrient digestibility of multi-enzyme-supplemented low-energy and -amino acid diets for growing and finishing pigs

Abstract Objective was to determine the effects of supplementing corn-soybean meal-based diets with a multi-enzyme on growth performance and apparent total tract digestibility (ATTD) of nutrients in growing pigs. A total of 276 pigs (BW = 33.99 ± 4.3 kg) were housed by sex in 45 pens of 6 or 7 pigs and fed 5 diets (9 pens/diet) in a randomized complete block design. Diets were positive control (PC); and negative control 1 (NC1) or negative control 2 (NC2) without or with multi-enzyme. The multi-enzyme used supplied at least 1,250, 860, 4,600, and 1,000 units of xylanase, β-glucanase, arabinofuranosidase and phytase per kilogram of diet, respectively. The PC was adequate in all nutrients according to NRC (2012) recommendations and had greater digestible P content than NC1 diet or NC2 diet by 0.134 percentage points. The NC1 diet had lower NE and digestible AA content than PC diet by 3%. The NC2 diet had lower NE and digestible AA content than PC diet by 5%. The diets were fed in 4 phases based on BW; Phase 1: 34–50 kg, Phase 2: 50–75 kg, Phase 3: 75–100 kg, and Phase 4: 100–120 kg. Nutrient digestibility was determined at the end of Phase 1. Overall (34–120 kg BW), pigs fed the PC and NC1 diets did not differ in ADG and ADFI. Pigs fed NC2 diet had lower (PPPP > 0.10). Supplemental multi-enzyme increased (P = 0.047) the ATTD of GE for NC2 diet. In conclusion, the NE and digestible AA and P can be lowered by ≤ 5% in multi-enzyme-supplemented diets without effects on growth performance pigs.

Impacts of stocking and its intensity on effective population size in Brook Charr (Salvelinus fontinalis) populations

Effective population size (Ne) is a measure of the genetic size of a population and a crucial parameter for wildlife population management since it is strongly related to retention of genetic diversity in time and/or to inbreeding levels. Many exploited fish populations are stocked with the purpose of increasing population sizes to sustain important fishing pressures. However, stocking hatchery-reared fish could at the same time increase population census size and decrease Ne. Our study aimed at characterizing how stocking affected Ne in supplemented populations of Brook Charr (Salvelinus fontinalis) in Quebec and at assessing how this relationship varied with the intensity of stocking (e.g. number of stocking events, number of fish stocked/ha, proportion of domestic genetic background). We estimated Ne with the linkage disequilibrium method in 54 populations (3361 sampled individuals analyzed at 20 microsatellites) with various levels of stocking intensity. We found that stocked lakes have significantly lower Ne than unstocked lakes. However, we found little evidence of an additional effect of stocking intensity on Ne of stocked lakes. Our results suggest that stocking may have a negative impact on Ne but that more intense stocking does not necessarily translate into lower Ne. However, even though low Ne in stocked populations could be attributed to an effect of stocking, it is also likely that stocked lakes consist of poor environments that translate into low Ne.

Differential Genetic Effect of the Norepinephrine Transporter Promoter Polymorphisms on Attention Problems in Clinical and Non-clinical Samples.

Among the monoaminergic modulatory neurotransmitters, norepinephrine is involved in task orienting, hence noradrenergic genetic variants have been studied in connection to attentional processes. The role of this catecholamine system is also highlighted by the selective norepinephrine transporter blocking atomoxetine, which has proved to be effective in the pharmacological treatment of Attention Deficit Hyperactivity Disorder (ADHD). In the present genetic association study three single nucleotide polymorphisms (rs28386840, rs2242446, rs3785143 SNPs) were analyzed from the 5′ region of the norepinephrine transporter (NET, SLC6A2) gene, which have been linked to ADHD previously. Attention problems scores of the mother-rated Child Behavior Checklist (CBCL) were used in separate analyses of 88 preschoolers (59.1% male, 6 years of age) recruited from the general population and 120 child psychiatry patients with ADHD diagnosis (85.8% male, age: 9.8 ± 2.9). The NET SNPs showed associations with attention problems, but the direction was different in the two groups. Regarding the promoter variant rs28386840, which showed the most consistent association, the T-allele-carrier patients with ADHD had lower CBCL attention problems scores compared to patients with AA genotype (p = 0.023), whereas T-allele-carriers in the community sample had more attention problems (p = 0.042). Based on previous reports of lower NE levels in ADHD children and the inverted-U shape effect of NE on cognitive functions, we propose that rs28386840 (-3081) T-allele, which is associated with lower NET expression (and potentially higher synaptic NE level) would support attention processes among ADHD patients (similarly as atomoxetine increases NE levels), whereas it would hinder cortical functions in healthy children.

Population genomics of Fundulus grandis exposed to oil from Deepwater Horizon

The April 2010 Deepwater Horizon (DWH) oil spill released over 4 million barrels of oil into northern Gulf of Mexico ecosystems. Due to the magnitude of the spill and observed effects from previous spills, the ecological impacts were predicted to be catastrophic. While negative effects of petroleum hydrocarbon exposure to fish have been documented at the organismal scale, most studies of fish assemblages have noted few, if any, DWH impacts. Our understanding of DWH effects is therefore limited by a disconnect in results reported at different organizational levels. We used population genomic tools to test hypotheses about population-level DWH impacts to Gulf Killifish (Fundulus grandis) in coastal Mississippi. Fundulus grandis is one of the most abundant marsh species in the northern Gulf of Mexico, and along with the sister species F. heteroclitus, has served as a model for toxicology research. We collected genotyping by sequencing data from four populations of F. grandis (two oiled and two not) to test predictions about DWH-related gene flow, demographics, genetic diversity and evidence of selection. Mississippi populations of F. grandis showed clear genetic structure, but there were few indicators (e.g. reduced genetic diversity, lower Ne estimates) consistent with large-scale mortality or migration related to DWH oil. Only one estimate of effective population size was reduced in oil-exposed populations and of the twenty outlier loci only two were in regions with potential adaptive significance (i.e., immune functions). While the toxic effects of oil on F. grandis at the organismal level is well established, the minimal impacts we detected to populations along the Mississippi coast likely reflects the complexity of the northern Gulf of Mexico and DWH oil spill. However, we do recognize that the patchiness of oil exposure and low genome coverage of the data limit our ability to conclude there were no DWH effects on these populations.

Census and contemporary effective population size of two populations of the protected Spanish Moon Moth (Graellsia isabellae)

Abstract Graellsia isabellae is a protected lepidopteran both in France and Spain; however, there has been considerable debate over its conservation status. Recent literature emphasised the need of monitoring population size in the different mountain ranges where this iconic species occurs. We used mark–capture–recapture and genotypes of nine molecular microsatellite markers to estimate the census (N) and contemporary effective population size (Ne) of two Spanish populations extending over similar size areas (10–15 km2): Puebla (Eastern Spain) and Ordesa (Western Pyrenees). Only adult males were captured and analysed, as sampling was based on the use of the synthesised female sex pheromone. Estimates of N were rather different in the two populations: 3398 males in Puebla (95% CI = 2875–4145) and 1500 in Ordesa (95% CI = 1229–1932), although the area occupied by the populations was larger and more densely forested in Ordesa than in Puebla. Several lines of evidence pointed to a moderate–large contemporary Ne at Puebla (173–178 individuals) and a one‐order of magnitude lower Ne at Ordesa (27–49). Thus, Ne/N ratios were very low (0.026 and 0.01 respectively). We recommend G. isabellae to be classified as of Least Concern under the IUCN criteria; however, the high temporal fragmentation index and the very low values of the Ne/N ratios obtained for this species, as compared with those recorded for most others, are usually taken as indicators of actual threat for their conservation. As a cautionary measure, managers should aim at maintaining gene flow by ensuring connectivity of Pinus sylvestris in these areas.

Another useful property of mtDNA: editorial comment on the highlighted article by Lou et al. (2018)

Mitochondrial DNA (mtDNA) has been the marker of choice since the advent of phylogeography, and for good reasons. Foremost, mtDNA is haploid, i.e., represented by a single variant of the molecule, as opposed to two sets of nuclear chromosomes in diploid organisms. This reduces effective population size (Ne) by half compared to nuclear DNA, and also facilitates sequencing and genotyping (all base pairs are expected to be homozygous in a haploid marker, circumventing the need to identify and distinguish alleles in heterozygotes, either physically through cloning or bioinformatically). Furthermore, contrary to the nuclear genome that is transmitted by both parents, mtDNA is maternally inherited. This reduces Ne by another half, resulting in an expected Ne for mtDNA that is a fourth of nuclear DNA. Lower Ne results in stronger genetic drift, providing higher resolution for phylogeographic analysis. In the era of whole genome sequencing (WGS), these advantages of mtDNA are balanced by the much larger volume of data provided by the nuclear genome. Yet, another property of mtDNA is that cells typically harbor many copies of the mitochondrial genome versus just a few of the nuclear genome, resulting in higher sequencing coverage for mtDNA than for nuclear DNA. Lou et al. (2018) leveraged this property to recover the full mitochondrial genomes of 189 Atlantic silversides (Menidia menidia) at a mean coverage of 153× from a low-coverage (1.3×) WGS experiment (Therkildsen and Palumbi 2017). They carefully addressed a number of potential issues with mtDNA, including the fact that it is a circular molecule (which complicates mapping in the absence of edges) and the possibility of heteroplasmy (the occurrence of several mtDNA variants) or mitochondrial insertions into the nuclear DNA. The M. menidia mitochondrial genome was 16,454 base pairs long, providing significantly more data and phylogeographic resolution than an earlier Marine Biology study based on a 340 base pair segment of the mtDNA control region (Mach et al. 2011). It also provided the opportunity to search for signs of selection at the 13 protein-coding genes present in the mtDNA and apply approximate Bayesian computation (ABC) analysis for demographic inference. Yet notwithstanding its many advantages, mtDNA also comes with a number of limitations. One generalization emerging from whole genome analysis is that evolutionary histories vary along the genome. In this regard, as a single molecule that lacks recombination, mtDNA essentially behaves as—and provides a sample size of—one locus. A related matter is that in the presence of whole genome data, and particularly high-coverage data, the gain from adding mtDNA may be marginal unless there is a specific biological motivation to do so such as mito-nuclear interactions or sex-biased dispersal. The analysis of the nuclear genomic data will allow to establish to what extent this applies to M. menidia.

Effective Population Size Differences in Calomys musculinus, the Host of Junín Virus: Their Relationship with the Epidemiological History of Argentine Hemorrhagic Fever.

Argentine hemorrhagic fever (AHF) is a serious endemic disease in Argentina, produced by Junín virus, whose host is the Sigmodontinae rodent Calomys musculinus. Within the endemic area, human incidence and proportion of infected rodents remains high for 5-10 years after the first appearance of the disease (epidemic [E] zone) and then gradually declines to sporadic cases (historic [H] zone). We tested the hypothesis that host populations within the E zone are large and well connected by gene flow, facilitating the transmission and maintenance of the virus, whereas those in the H and nonendemic (NE) zones are small and isolated, with the opposite effect. We estimated parameters affected by levels of gene flow and population size in 14 populations of C. musculinus: population effective size (Ne), genetic variability, and mean relatedness. Our hypothesis was not supported: the lowest levels of variability and of Ne and the highest genetic relatedness among individuals were found in the H zone. Populations from the NE zone displayed opposite results, whereas those in the E zone showed intermediate values. If we consider that populations are first NE, then E, and finally H, a correlative decrease in Ne was observed. Chronically infected females have a low reproductive success. We propose that this would lower Ne because each cohort would originate from a fraction of females of the previous generation, and affect other factors such as proportion of individuals that develop acute infection, probability of viral transmission, and evolution of virulence, which would explain, at least partly, the changing incidence of AHF.

3D electron density specification to support LEO and MEO satellite applications

The TaD three-dimensional (3D) electron density (Ne) specification model is compared with in situ measured Ne by the Instrument Sonde Langmuir (ISL) onboard DEMETER satellite. For this purpose, over 2000 parts of satellite orbits over the European region in the years 2009–2011 were selected. For each measured Ne value, a corresponding value was calculated with the TaD 3D model, using maps of foF2 and hmF2 from ionosondes and maps of TEC values from CODE software. To compare modelled and measured Ne, the relative to the model deviation between the two quantities was calculated. The comparisons exceeded the total number of 180,000. The main result shows that the modelled Ne extracted by the TaD profiles that have been calculated through adjustment with the TEC CODE parameters, exhibit significant deviations from the measured Ne at the satellite orbit height. Histograms of the relative deviations relNe show an average offset of 50–60%, while the standard deviation is around 30%. Separate analysis was performed to compare the modelled Ne over 11 ionosonde stations with the measured Ne by the satellite over the ionosonde locations and thus to eliminate the error inferred from the mapping procedure. Here the TaD profiles were adjusted with both the TEC CODE parameters and with TEC values extracted with the single GNSS station solution software with data from GNSS receivers co-located with the ionosondes. In the latter case, the lower TEC values compared to those of TEC CODE yield lower modelled Ne which resulted to smaller deviations with the satellite data. The present study reveals the low consistency between different measurements involved in modeled reconstruction. The comparison presented here shows the importance of assessing the inconsistency between different measurements being assimilated or ingested in the 3D Ne models. Probable inconsistency of different data can create a wrong base for further geophysical studies.

Exploring drift effects in TCV single-null plasmas with the UEDGE code

This paper explores the effects of particle drifts across the magnetic field in TCV single-null plasmas using the two-dimensional edge plasma transport code UEDGE. In particular, it aims to reproduce a double-peaked density target profile, a feature which has been observed both at JET and in a TCV forward-field ( drift of core ions towards the X-point) discharge. Initial simulations are performed with drift effects turned off. This allows identification of the input parameters that strongly influence the computed steady-state but are not well known from the experiment. Including cross-field drifts self-consistently in the simulations brings computed profiles at the inner target closer to the experiment, with the double peak being reproduced for the density. In agreement with the experiment, simulations of a similar reversed-field shot yield lower ne and higher Te at the inner target, as well as unchanged temperatures at the outer plate. However, several discrepancies remain. In the forward field case, the inner target density peak near the separatrix is much sharper than seen experimentally. Furthermore, simulations show a strong dependence of the outer plate density and of the outer/inner power sharing on toroidal field direction. Experimentally, no such dependencies are observed. In the simulations, the changes of target profiles with field direction are mainly due to E × B drifts in the divertor region. While these simulations highlight the importance of E × B drifts in these TCV plasmas, the remaining differences with the experiment indicate that their role is overestimated in the simulations.

Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

BackgroundInvestments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Ne) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. The estimation of Ne can be determined via genetic markers and requires knowledge of genetic distances between these markers. Single nucleotide polymorphisms (SNP) data from a sample of 12,597 New Zealand crossbred and purebred sheep genotyped with the Illumina Ovine SNP50 BeadChip was used to perform a genome-wide scan of LD and Ne. Three methods to estimate genetic distances were investigated: 1) M1: a ratio fixed across the whole genome of one Megabase per centiMorgan; 2) M2: the ratios of genetic distance (using M3, below) over physical distance fixed for each chromosome; and, 3) M3: a genetic map of inter-SNP distances estimated using CRIMAP software (v2.503).ResultsThe estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower Ne results and higher LD decay. The results suggest that Ne has decreased since the development of sheep breeds in Europe and this reduction in Ne has been accelerated in the last three decades. The Ne estimated for five generations in the past ranged from 71 to 237 for Texel and Romney breeds, respectively. A low level of genetic kinship and inbreeding was estimated in those breeds suggesting avoidance of mating close relatives.ConclusionsM3 was considered the most accurate method to create genetic maps for the estimation of LD and Ne. The findings of this study highlight the history of genetic selection in New Zealand crossbred and purebred sheep and these results will be very useful to understand genetic diversity of the population with respect to genetic selection. In addition, it will help geneticists to identify genomic regions which have been preferentially selected within a variety of breeds and populations.

Re-evaluation of polyphase kinematic and 40Ar/39Ar cooling history of Moldanubian hot nappe at the eastern margin of the Bohemian Massif

A structural and geochronological 40Ar/39Ar study was performed in kilometre-scale middle and lower crustal lens-shaped domains dominated by a preserved subvertical foliation, surrounded by horizontally foliated migmatites. These domains occur within the Moldanubian nappe overlying the Brunia microcontinent at the eastern margin of the European Variscides. Three main deformation phases were recognized: subvertical S2 fabric trending NW–SE in lower crustal rocks and NE–SW in mid-crustal rocks. It is reworked by HT/MT horizontal fabric S3 along margins of crustal domains and in surrounding migmatites. S3 bears a prolate NE lineation parallel to the S2–S3 intersection in the lower crustal domain. In the middle crustal units, L3 is weak, connected to oblate strain and trends NE–SW parallel to the S2–S3 intersection. D4 non-coaxial shear deformation is mainly localized at the boundary between the Moldanubian nappe and Brunia and bears strong top to the NNE shear criteria. In order to constrain kinematics of the D3 deformation, strain modelling was performed to show that the Moldanubian hot nappe was frontally thrust over the Brunia indentor. The renewed D4 tangential movement only heterogeneously reactivates the horizontal S3. This evolution is recorded in 40Ar/39Ar amphibole cooling ages, which show two statistically significant Carboniferous peaks at ~342 and 332 Ma, which are also reflected by published detrital muscovite 40Ar/39Ar ages in the adjacent foreland basin. This geochronological record is correlated with progressive erosion of the topographically elevated upper crustal part of the Moldanubian nappe during D3 frontal thrusting, followed by greenschist facies D4 transpressive reactivation and subsequent erosion of high-grade parts of the nappe.

Sex change and effective population size: implications for population genetic studies in marine fish.

Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected from two ecologically similar species living along the eastern coast of South Africa: one gonochoristic, the 'santer' sea bream Cheimerius nufar, and one protogynous (female-first) sex changer, the 'slinger' sea bream Chrysoblephus puniceus. For both species, no evidence of genetic structuring, nor significant variation in genetic diversity, was found in the study area. Estimates of contemporary Ne were significantly lower in the protogynous species, but the same pattern was not apparent over historical timescales. Overall, our results show that sequential hermaphroditism may affect Ne differently over varying time frames, and that demographic signatures inferred from genetic markers with different inheritance modes also need to be interpreted cautiously, in relation to sex-changing life histories.

New evidence of wavefield polarization on fault zone in the lower NE slope of Mt. Etna

Fault zones are generally characterized by a damage zone, formed by highly fractured materials, that is seismically characterized by low velocity and rigidity compared to the host rock. Such geometrical setting, coupled with impedance contrast, lead to the development of local amplification of the ground motion and directional effects. In the present study, the results of measurements performed in the lower north-eastern area of Mt. Etna are shown and discussed. Ambient noise data were recorded and processed through the horizontal to vertical spectral ratio technique, setting into evidence directional effects and providing a direct estimate of the polarization angle as well. The data were recorded along and across the Piedimonte-Fiumefreddo fault system, a set of NE-SW trending extensional segmented faults, that is flanked by small conjugate segments and is accompanied by several WNW-ESE oriented minor faults and fractures of the Pernicana fault system.Results point out that in most of the investigated sites the polarization effects are nearly perpendicular with respect to the minor faults, striking WNW-ESE. This highlight that the local extensional deformation field, related to the shear zone of the Pernicana fault system, plays an important role and it appears as the predominant one in the seismic response that characterize this tectonically complicated area.

Importance of the geographic barriers to promote gene drift and avoid pre- and post-Columbian gene flow in Mexican native groups: Evidence from forensic STR Loci.

To analyze the origin, structure, relationships, and recent admixture in Mexican Native groups based on 15 STRs commonly used in human identification. We analyzed 39 Mexican Native population samples using STR databases based on the AmpFlSTR® Identifiler kit (n = 3,135), including Mexican-Mestizos (admixed), European and African populations, as reference. Based upon effective population size (Ne) differences, Native groups were clustered into three regions: i) Center-Southeast groups, characterized by larger Ne, migration rate (Nm), genetic diversity (He), and relative homogeneity principally in the Yucatan Peninsula; ii) Isolated southern groups from Chiapas and Oaxaca, characterized by lower Ne, Nm, and He (i.e. higher isolation and genetic differentiation); iii) North-Northwest groups, which are similar to the previous group but are characterized by generating the widest gene flow barrier in the Pre-Hispanic Mexican territory, and currently by elevated admixture in some northern Native groups. Despite the relative congruence between genetic relationships with cultural, linguistic, geographic criteria, these factors do not explain the present-day population structure of Native groups, excepting in those linguistically related to the Mayan that show higher homogeneity. The Isolation by distance model was demonstrated at long distances (>1,500 km), whereas geographic isolation stands as a determining factor to avoid both non-indigenous admixture and bottleneck processes. Different dynamics of gene flow and drift were observed among Mexican Native groups, highlighting the geographic barriers (mountains, canyons and jungle regions) as the main factor differentiating Pre-Hispanic populations, and eventually helping to avoid Post-European contact admixture and population bottleneck. Am J Phys Anthropol 160:298-316, 2016. © 2016 Wiley Periodicals, Inc.

Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences.

Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne ) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) - black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne . Our results highlight the usefulness of the psmc approach in investigating species' reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.

The transition from large-magnitude extension to distributed dextral faulting in the Buckskin-Rawhide metamorphic core complex, west-central Arizona

Brittle fault data from the Buckskin-Rawhide metamorphic core complex, west-central Arizona, document the Miocene transition from large-magnitude, NE directed extension to distributed E-W extension and dextral faulting. The Buckskin-Rawhide detachment fault locally records a clockwise rotation of the slip direction from dominant top-NE directed slip to ENE and E directed slip during the last stages of activity. Postmylonitic brittle deformation is dominated by normal and dextral slip along moderately to steeply NE dipping faults. Relative timing relationships indicate that most postmylonitic normal faulting was coeval with middle Miocene detachment fault slip, whereas dextral and oblique dextral faulting postdates detachment fault slip (post ~11 Ma). Based on the persistent SW dip of lower plate fabrics and NE dip of abundant normal faults, the amount of NE-SW brittle extension across the mylonitic lower plate is estimated to be 20–30% in several areas. The end of detachment faulting in the Buckskin-Rawhide metamorphic core complex was marked by a transition to dominantly E-W extension and associated dextral-normal faulting. At least 10 NE dipping postdetachment faults record ~0.1–1 km dextral or oblique dextral displacement. The cumulative amount of dextral shear across the core complex is probably 7–9 km, which is the amount needed to restore the topographic trend of lower plate corrugations into alignment with the dominant extension direction. Postdetachment dextral/transtensional faulting across the core complex reflects the increasing influence of the diffuse Pacific-North America transform plate boundary toward the end of the middle Miocene.