Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes

Life-history traits vary substantially across species, and have been demonstrated to affect substitution rates. We compute genomewide, branch-specific estimates of male mutation bias (the ratio of male-to-female mutation rates) across 32 mammalian genomes and study how these vary with life-history traits (generation time, metabolic rate, and sperm competition). We also investigate the influence of life-history traits on substitution rates at unconstrained sites across a wide phylogenetic range. We observe that increased generation time is the strongest predictor of variation in both substitution rates (for which it is a negative predictor) and male mutation bias (for which it is a positive predictor). Although less significant, we also observe that estimates of metabolic rate, reflecting replication-independent DNA damage and repair mechanisms, correlate negatively with autosomal substitution rates, and positively with male mutation bias. Finally, in contrast to expectations, we find no significant correlation between sperm competition and either autosomal substitution rates or male mutation bias. Our results support the important but frequently opposite effects of some, but not all, life history traits on substitution rates. KEY WORDS: Generation time, genome evolution, metabolic rate, sperm competition.

Simulated variations in atmospheric CO2 over a Wisconsin forest using a coupled ecosystem-atmosphere model

Ecosystem fluxes of energy, water, and CO2 result in spatial and temporal variations in atmospheric properties. In principle, these variations can be used to quantify the fluxes through inverse modelling of atmospheric transport, and can improve the understanding of processes and falsifiability of models. We investigated the influence of ecosystem fluxes on atmospheric CO2 in the vicinity of the WLEF-TV tower in Wisconsin using an ecophysiological model (Simple Biosphere, SiB2) coupled to an atmospheric model (Regional Atmospheric Modelling System). Model parameters were specified from satellite imagery and soil texture data. In a companion paper, simulated fluxes in the immediate tower vicinity have been compared to eddy covariance fluxes measured at the tower, with meteorology specified from tower sensors. Results were encouraging with respect to the ability of the model to capture observed diurnal cycles of fluxes. Here, the effects of fluxes in the tower footprint were also investigated by coupling SiB2 to a high-resolution atmospheric simulation, so that the model physiology could affect the meteorological environment. These experiments were successful in reproducing observed fluxes and concentration gradients during the day and at night, but revealed problems during transitions at sunrise and sunset that appear to be related to the canopy radiation parameterization in SiB2.

Feeding selectivity of ichthyofauna in a tropical stream: space-time variations in trophic plasticity

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Temporal patterns of parasitism in Diatraea saccharalis Fabr. (Lep., Crambidae) populations at different spatial scales in sugarcane fields in Brazil

Biological control of Diatraea saccharalis is regarded as one of the best examples of successful classical biological control in Brazil. Since the introduction of the exotic parasitoid, Cotesia flavipes, from Pakistan at the beginning of the 1970s, decrease in D. saccharalis infestation in sugarcane fields has been attributed to the effectiveness of this agent. Recently, the native Tachinidae fly parasitoids (Lydella minense and Paratheresia claripalpis) have also been implicated in this success. However, quantitative data confirming the actual contribution of these agents to the control of D. saccharalis are rather limited. The purpose of this study was to investigate the dynamics of the interactions between D. saccharalis and its parasitoids, emphasizing the temporal patterns of parasitism. To investigate this question, a large data set comprising information collected from two sugarcane mills located in the state of São Paulo, Brazil (Barra and Sao Joao sugarcane mills), was analysed. Basically, the data set contained monthly information about the number of D. saccharalis larvae and their parasitoids in each sample (man-hour per sample), the sugarcane varieties cultivated, the age of the sugarcane plants (only at the Sao Joao sugarcane mill) as well as the sugarcane cut at sampling time. The data were collected from March 1984 to March 1997 and from May 1982 to December 1996 for the Barra and Sao Joao sugarcane mills, respectively. Temporal inverse density-dependent parasitism was predominant for both parasitoid species with respect to all spatial scales. Although the temporal pattern of parasitism was not directly density dependent, it was evident that the tachinids and C. flavipes presented positive numerical responses according to variations in D. saccharalis densities through time.

Effects of nanoscale spatial inhomogeneity in strongly correlated systems

We calculate ground-state energies and density distributions of Hubbard superlattices characterized by periodic modulations of the on-site interaction and the on-site potential. Both density-matrix renormalization group and density-functional methods are employed and compared. We find that small variations in the on-site potential v(i) can simulate, cancel, or even overcompensate effects due to much larger variations in the on-site interaction U-i. Our findings highlight the importance of nanoscale spatial inhomogeneity in strongly correlated systems, and call for a reexamination of model calculations assuming spatial homogeneity.

Phytoplankton community response to hydrological variations in oxbow lakes with different levels of connection to a tropical river

Changes to the structure of the phytoplankton community and to the physical and chemical variables of the water were investigated in oxbow lakes with different levels of connection to a tropical river and subject to annual hydrological pulse variations. The selected lentic environments are located at the mouth region of the main tributary in a reservoir built for water storage and electric power generation. The temporal variation of phytoplankton in the studied lentic environments can be attributed mainly to the hydrological level of the river. A similar variation pattern of the ecological attributes was observed in the structure of the phytoplankton community in the connected lakes and Paranapanema River, evidencing the high degree of association that the lacustrine systems maintain with the river. The highest values of richness and diversity for connected environments were observed at the end of the emptying period and in the drought. However, considering the isolated lake, the highest values of these attributes were recorded during the flooding period. © 2013 Springer Science+Business Media Dordrecht.

Tree species community spatial structure in a terra firme Amazon forest, Brazil

All trees with diameter at breast height dbh >= 10.0 cm were stem-mapped in a "terra firme" tropical rainforest in the Brazilian Amazon, at the EMBRAPA Experimental Site, Manaus, Brazil. Specifically, the relationships of tree species with soil properties were determined by using canonical correspondence analyses based on nine soil variables and 68 tree species. From the canonical correspondence analyses, the species were grouped into two groups: one where species occur mainly in sandy sites, presenting low organic matter content; and another one where species occur mainly in dry and clayey sites. Hence, we used Ripley's K function to analyze the distribution of species in 32 plots ranging from 2,500 m(2) to 20,000 m(2) to determine whether each group presents some spatial aggregation as a soil variations result. Significant spatial aggregation for the two groups was found only at over 10,000 m(2) sampling units, particularly for those species found in clayey soils and drier environments, where the sampling units investigated seemed to meet the species requirements. Soil variables, mediated by topographic positions had influenced species spatial aggregation, mainly in an intermediate to large distances varied range (>= 20 m). Based on our findings, we conclude that environmental heterogeneity and 10,000 m(2) minimum sample unit sizes should be considered in forest dynamic studies in order to understand the spatial processes structuring the "terra firme" tropical rainforest in Brazilian Amazon.

Molecular measurement of BCR-ABL transcript variations in chronic myeloid leukemia patients in cytogenetic remission

Abstract Background The monitoring of BCR-ABL transcript levels by real-time quantitative polymerase chain reaction (RT-qPCR) has become important to assess minimal residual disease (MRD) and standard of care in the treatment of chronic myeloid leukemia (CML). In this study, we performed a prospective, sequential analysis using RT-qPCR monitoring of BCR-ABL gene rearrangements in blood samples from 91 CML patients in chronic phase (CP) who achieved complete cytogenetic remission (CCyR) and major molecular remission (MMR) throughout imatinib treatment. Methods The absolute level of BCR-ABL transcript from peripheral blood was serially measured every 4 to 12 weeks by RT-qPCR. Only level variations > 0.5%, according to the international scale, was considered positive. Sequential cytogenetic analysis was also performed in bone marrow samples from all patients using standard protocols. Results Based on sequential analysis of BCR-ABL transcripts, the 91 patients were divided into three categories: (A) 57 (62.6%) had no variation on sequential analysis; (B) 30 (32.9%) had a single positive variation result obtained in a single sample; and (C) 4 (4.39%) had variations of BCR-ABL transcripts in at least two consecutive samples. Of the 34 patients who had elevated levels of transcripts (group B and C), 19 (55.8%) had a < 1% of BCR-ABL/BCR ratio, 13 (38.2%) patients had a 1% to 10% increase and 2 patients had a >10% increase of RT-qPCR. The last two patients had lost a CCyR, and none of them showed mutations in the ABL gene. Transient cytogenetic alterations in Ph-negative cells were observed in five (5.5%) patients, and none of whom lost CCyR. Conclusions Despite an increase levels of BCR-ABL/BCR ratio variations by RT-qPCR, the majority of CML patients with MMR remained in CCyR. Thus, such single variations should neither be considered predictive of subsequent failure and nor an indication for altering imatinib dose or switching to second generation therapy. Changing of imatinib on the basis of BCR-ABL/BCR% sustained increase and mutational studies is a prudent approach for preserving other therapeutic options in imatinib-resistant patients.

Global and regional sea level variations in the recent past and future: insight from observations and modeling

This work is focused on the analysis of sea–level change (last century), based mainly on instrumental observations. During this period, individual components of sea–level change are investigated, both at global and regional scales. Some of the geophysical processes responsible for current sea-level change such as glacial isostatic adjustments and current melting terrestrial ice sources, have been modeled and compared with observations. A new value of global mean sea level change based of tide gauges observations has been independently assessed in 1.5 mm/year, using corrections for glacial isostatic adjustment obtained with different models as a criterion for the tide gauge selection. The long wavelength spatial variability of the main components of sea–level change has been investigated by means of traditional and new spectral methods. Complex non–linear trends and abrupt sea–level variations shown by tide gauges records have been addressed applying different approaches to regional case studies. The Ensemble Empirical Mode Decomposition technique has been used to analyse tide gauges records from the Adriatic Sea to ascertain the existence of cyclic sea-level variations. An Early Warning approach have been adopted to detect tipping points in sea–level records of North East Pacific and their relationship with oceanic modes. Global sea–level projections to year 2100 have been obtained by a semi-empirical approach based on the artificial neural network method. In addition, a model-based approach has been applied to the case of the Mediterranean Sea, obtaining sea-level projection to year 2050.

Holocene flood frequency across the Central Alps – solar forcing and evidence for variations in North Atlantic atmospheric circulation

The frequency of large-scale heavy precipitation events in the European Alps is expected to undergo substantial changes with current climate change. Hence, knowledge about the past natural variability of floods caused by heavy precipitation constitutes important input for climate projections. We present a comprehensive Holocene (10,000 years) reconstruction of the flood frequency in the Central European Alps combining 15 lacustrine sediment records. These records provide an extensive catalog of flood deposits, which were generated by flood-induced underflows delivering terrestrial material to the lake floors. The multi-archive approach allows suppressing local weather patterns, such as thunderstorms, from the obtained climate signal. We reconstructed mainly late spring to fall events since ice cover and precipitation in form of snow in winter at high-altitude study sites do inhibit the generation of flood layers. We found that flood frequency was higher during cool periods, coinciding with lows in solar activity. In addition, flood occurrence shows periodicities that are also observed in reconstructions of solar activity from C-14 and Be-10 records (2500-3000, 900-1200, as well as of about 710, 500, 350, 208 (Suess cycle), 150, 104 and 87 (Gleissberg cycle) years). As atmospheric mechanism, we propose an expansion/shrinking of the Hadley cell with increasing/decreasing air temperature, causing dry/wet conditions in Central Europe during phases of high/low solar activity. Furthermore, differences between the flood patterns from the Northern Alps and the Southern Alps indicate changes in North Atlantic circulation. Enhanced flood occurrence in the South compared to the North suggests a pronounced southward position of the Westerlies and/or blocking over the northern North Atlantic, hence resembling a negative NAO state (most distinct from 4.2 to 2.4 kyr BP and during the Little Ice Age). South-Alpine flood activity therefore provides a qualitative record of variations in a paleo-NAO pattern during the Holocene. Additionally, increased South Alpine flood activity contrasts to low precipitation in tropical Central America (Cariaco Basin) on the Holocene and centennial time scale. This observation is consistent with a Holocene southward migration of the Atlantic circulation system, and hence of the ITCZ, driven by decreasing summer insolation in the Northern hemisphere, as well as with shorter-term fluctuations probably driven by solar activity. (C) 2013 Elsevier Ltd. All rights reserved.

Variations in coastal fish species composition captured by traps in Romsdalsfjord, Western Norway

Fish traps are widely used in Norwegian fjords, especially those designed for monitoring salmonid populations in the marine environment, although many other marine fish species are also captured. The composition and spatio-temporal variations of fish species captured by fish traps were monitored in five different coastal locations throughout the Romsdalsfjord region, Western Norway, from May to August during the three consecutive years (2011–2013). Twenty-three fish species were captured by traps in coastal waters, both resident and migratory fishes. The most common fish and with greater catchability were saithe (Pollachis virens) and sea trout (Salmo trutta), followed by cod (Gadus morhua), pollack (P. pollachius), herring (Clupea harengus) and mackerels (Trachurus trachurus and Scomber scombrus). However, the captured assemblage presented great spatial and seasonal variations, in terms of mean daily catch, probably associated with hydrographical conditions and migrational patterns. Information obtained in this study will help us to better understand the compositions and dynamic of coastal fish populations inhabiting Norwegian coastal waters. In addition, traps are highly recommended as a management tool for fish research (e.g. fish-tagging experiments, mark and recapture) and conservation purposes (coastal use and fisheries studies).

Short-term variations in radiolarian faunal dsitribution in the eastern equatorial Pacific

Two short time intervals centered at 2.3 and 4.7 Ma were studied to investigate short-term variations in surface-ocean processes as indicated by changes in the radiolarian microfossil population. These time intervals represent two different settings of late Neogene climate. The older interval represents a time when tropical circulation between the Pacific and Atlantic oceans was not blocked by the Isthmus of Panama, whereas the younger interval represents a time when Northern Hemisphere glaciation was present but did not display the dominance of the 100,000-yr cycle that characterizes the late Pleistocene. The younger time slice at 2.3 Ma was sampled at all Leg 138 sites except Site 844, where significant reworking was evident. All sites except 844, 853, and 854 were sampled for the older time slice. Samples were taken at 10- to 20-cm intervals at each site and spanned a GRAPE density maximum and minimum. Thus, it was possible to investigate whether the changes in carbonate content (as indicated by GRAPE density) were associated with changes in surface-ocean conditions (indicated by radiolarian assemblage variations). For both time slices, the radiolarian data indicate that intervals of decreased carbonate content are periods of cooler water conditions and possibly enhanced biogenic production. Times of increased carbonate content are associated with inferred warmer oceanographic conditions, as indicated by the dominance of tropical assemblages at 2.3 Ma and tropical and western Pacific assemblages during the time slice centered at 4.8 Ma. However, the spatial patterns of change during each time slice show a distinct difference in the mapped patterns of radiolarian assemblage dominance. The older time slice, representing a period before the closing of the Isthmus of Panama, shows more zonal patterns presumably associated with a more zonal character of equatorial circulation. After the closing of the isthmus, the shifts in faunal patterns between times of high and low carbonates are characterized by shifts in the dominance of the tropical and transitional assemblages, respectively, throughout the region.

Variations in seafloor depth estimates under different swath-width characteristics of submarine structures in the California Borderlands

Senior thesis written for Oceanography 445

Explaining variations in the knowledge economy in three small wealthy countries

At a broad level, it has been shown that different institutional contexts, policy regimes and business systems affect the kinds of activities in which a nation specialises. This paper is concerned with the way in which different national business systems affect the nature of participation of a nation in the knowledge economy. The paper seeks to explain cross-national variations in the knowledge economy in the Australia, Denmark and Sweden with reference to dominant characteristics of the business system. Although Australia, Denmark and Sweden are all small wealthy countries, they each have quite distinctive business systems. Australia has been regarded as a variant of the competitive business system and has generally been described as an entrepreneurial economy with a large small firm population. In contrast Sweden has a coordinated business system that has favoured large industrial firms. The Danish variant of the coordinated model, with its well-developed vocational training system, is distinguishable by its large population of networked small and medium size enterprises. The three countries also differ significantly on two dimensions of participation in the knowledge economy. First, there is cross-national variation in patterns of specialisation in knowledge intensive industries and services. Second, the institutional infrastructure of the knowledge economy (or the existing stock of knowledge and competence in the economy, the potential for generation and diffusion a new knowledge and the capacity for commercialisation of new ideas) differs across the three countries. This paper seeks to explain variations in these two dimensions of the knowledge economy with reference to characteristics of the business system in the three countries.