A balance index for phylogenetic trees based on rooted quartets

We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of leaves. We determine its maximum and minimum values for arbitrary and bifurcating trees, and we provide exact formulas for its expected value and variance on bifurcating trees under Ford’s α-model and Aldous’ β-model and on arbitrary trees under the α– γ-model.Peer ReviewedPostprint (author's final draft

A new balance index for phylogenetic trees

Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over all pairs of different leaves, of the depth of their least common ancestor. This index makes sense for arbitrary trees, can be computed in linear time and it has a larger range of values and a greater resolution power than other indices like Colless' or Sackin's. We compute its maximum and minimum values for arbitrary and binary trees, as well as exact formulas for its expected value for binary trees under the Yule and the uniform models of evolution. As a byproduct of this study, we obtain an exact formula for the expected value of the Sackin index under the uniform model, a result that seems to be new in the literature.Comment: 24 pages, 2 figures, preliminary version presented at the JBI 201

Spatial and temporal variability of discards indicators and fishery factors affecting otter-trawl fishery in the spanish Mediterranean sea

A set of diversity indices were studied from data of observers on board two Mediterranean trawlers from 2001 to 2009. These diversity indices comprise relationships between total catch, landing and discard fractions to explore the accuracy of the estimates and to analyse the series trends using different methods, such as ARIMA. The hypothesis tested was that diversity indicators give a good representation of the changes produced in impacted bottom‐trawl areas, providing a reasonable fit of the data. ARIMA models are useful because they handle time-correlated modelling and forecasting. These techniques can also reveal changes in total catch as well changes in catch composition, probably induced by changes in effort fishery, seasonal (time) fluctuations, and environmental or climatic processes. Contrasted trends were also compared with survey data by MEDITS Mediterranean trawl survey time‐series indicator

Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling

Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature of genetic changes that characterise lethal metastatic disease is poorly understood. Here, we analyze the evolution of human melanoma progressing from early to late disease in 13 patients by sampling their tumours at multiple sites and times. Whole exome and genome sequencing data from 88 tumour samples reveals only limited gain of point mutations generally, with net mutational loss in some metastases. In contrast, melanoma evolution is dominated by whole genome doubling and large-scale aneuploidy, in which widespread loss of heterozygosity sculpts the burden of point mutations, neoantigens and structural variants even in treatment-naïve and primary cutaneous melanomas in some patients. These results imply that dysregulation of genomic integrity is a key driver of selective clonal advantage during melanoma progression

Clinical and structural brain correlates of hypomimia in early-stage Parkinson's disease

Altres ajuts: acord transformatiu CRUE-CSICBackground and purpose: Reduced facial expression of emotions is a very frequent symptom of Parkinson's disease (PD) and has been considered part of the motor features of the disease. However, the neural correlates of hypomimia and the relationship between hypomimia and other non-motor symptoms of PD are poorly understood. Methods: The clinical and structural brain correlates of hypomimia were studied. For this purpose, cross-sectional data from the COPPADIS study database were used. Age, disease duration, levodopa equivalent daily dose, Unified Parkinson's Disease Rating Scale part III (UPDRS-III), severity of apathy and depression and global cognitive status were collected. At the imaging level, analyses based on gray matter volume and cortical thickness were used. Results: After controlling for multiple confounding variables such as age or disease duration, the severity of hypomimia was shown to be indissociable from the UPDRS-III speech and bradykinesia items and was significantly related to the severity of apathy (β = 0.595; p < 0.0001). At the level of neural correlates, hypomimia was related to motor regions brodmann area 8 (BA 8) and to multiple fronto-temporo-parietal regions involved in the decoding, recognition and production of facial expression of emotions. Conclusion: Reduced facial expressivity in PD is related to the severity of symptoms of apathy and is mediated by the dysfunction of brain systems involved in motor control and in the recognition, integration and expression of emotions. Therefore, hypomimia in PD may be conceptualized not exclusively as a motor symptom but as a consequence of a multidimensional deficit leading to a symptom where motor and non-motor aspects converge

Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations

Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML

Measurement of forward W and Z boson production in pppp collisions at s=8 \sqrt{s}=8 TeV

Measurements are presented of electroweak boson production using data from $pp$ collisions at a centre-of-mass energy of $\sqrt{s} = 8\mathrm{\,Te\kern -0.1em V}$. The analysis is based on an integrated luminosity of $2.0\mathrm{\,fb}^{-1}$ recorded with the LHCb detector. The bosons are identified in the $W\rightarrow\mu\nu$ and $Z\rightarrow\mu^{+}\mu^{-}$ decay channels. The cross-sections are measured for muons in the pseudorapidity range $2.0 20{\mathrm{\,Ge\kern -0.1em V\!/}c}$ and, in the case of the $Z$ boson, a dimuon mass within $60 < M_{\mu^{+}\mu^{-}} < 120{\mathrm{\,Ge\kern -0.1em V\!/}c^{2}}$. The results are \begin{align*} \sigma_{W^{+}\rightarrow\mu^{+}\nu} &= 1093.6 \pm 2.1 \pm 7.2 \pm 10.9 \pm 12.7{\rm \,pb} \, , \sigma_{W^{-}\rightarrow\mu^{-}\bar{\nu}} &= \phantom{0}818.4 \pm 1.9 \pm 5.0 \pm \phantom{0}7.0 \pm \phantom{0}9.5{\rm \,pb} \, , \sigma_{Z\rightarrow\mu^{+}\mu^{-}} &= \phantom{00}95.0 \pm 0.3 \pm 0.7 \pm \phantom{0}1.1 \pm \phantom{0}1.1{\rm \,pb} \, , \end{align*} where the first uncertainties are statistical, the second are systematic, the third are due to the knowledge of the LHC beam energy and the fourth are due to the luminosity determination. The evolution of the $W$ and $Z$ boson cross-sections with centre-of-mass energy is studied using previously reported measurements with $1.0\mathrm{\,fb}^{-1}$ of data at $7\mathrm{\,Te\kern -0.1em V}$. Differential distributions are also presented. Results are in good agreement with theoretical predictions at next-to-next-to-leading order in perturbative quantum chromodynamics.Comment: All figures and tables, along with any supplementary material and additional information, are available at https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2015-049.htm

Long-term climatic influences on the physiological condition of the red shrimp Aristeus antennatus in the Western Mediterranean Sea

Changes in the physiological condition (represented by Kn = body weight/length predicted weight) of the deep-sea shrimp Aristeus antennatus associated with the warming and rising salinity trends in the western Mediterranean were analyzed to explore how deep-sea populations can reconfigure their biology to match the changes in ocean conditions. Two slope areas around the Balearic Islands (Western Mediterranean Sea) were analyzed using sampling data and generalized additive models. The 23 yr time series of monthly Kn estimates shows 2 different aspects of the life history of A. antennatus, corresponding to 2 different seasonal periods. The Kn series from June through September reflects the shrimps’ reproductive condition to the north of the Islands, while samples from October through May represent a period of low gonad weight and high hepatosomatic indices to the south of the Islands. Oceanographic variables used to construct models and seek relationships with changes in Kn were salinity, temperature, and dissolved oxygen in the Levantine Intermediate Water and Western Mediterranean Deep Water layers, and chlorophyll a satellite imagery data. The North Atlantic Oscillation and the Eastern Atlantic index were used as climatic indicators. Physiologic condition during the winter fattening periods decreased over the time series and was negatively correlated with increasing salinity. During the summer reproductive periods, the best-fitting models show a year-on-year effect and a significant probability of effects on condition from oligotrophication. These results suggest that increasing salinity at depth, which ultimately increases oligotrophy, may cause changes in physiological conditionVersión del editor1,99

Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

Abstract Background The CO2-concentrating mechanism associated to Crassulacean acid metabolism (CAM) alters the catalytic context for Rubisco by increasing CO2 availability and provides an advantage in particular ecological conditions. We hypothesized about the existence of molecular changes linked to these particular adaptations in CAM Rubisco. We investigated molecular evolution of the Rubisco large (L-) subunit in 78 orchids and 144 bromeliads with C3 and CAM photosynthetic pathways. The sequence analyses were complemented with measurements of Rubisco kinetics in some species with contrasting photosynthetic mechanism and differing in the L-subunit sequence. Results We identified potential positively selected sites and residues with signatures of co-adaptation. The implementation of a decision tree model related Rubisco specific variable sites to the leaf carbon isotopic composition of the species. Differences in the Rubisco catalytic traits found among C3 orchids and between strong CAM and C3 bromeliads suggested Rubisco had evolved in response to differing CO2 concentration. Conclusions The results revealed that the variability in the Rubisco L-subunit sequence in orchids and bromeliads is composed of coevolving sites under potential positive adaptive signal. The sequence variability was related to δ13C in orchids and bromeliads, however it could not be linked to the variability found in the kinetic properties of the studied species

Exploring molecular evolution of Rubisco in C3 and CAM Orchidaceae and Bromeliaceae

[eng] Background: The CO2-concentrating mechanism associated to Crassulacean acid metabolism (CAM) alters the catalytic context for Rubisco by increasing CO2 availability and provides an advantage in particular ecological conditions. We hypothesized about the existence of molecular changes linked to these particular adaptations in CAM Rubisco. We investigated molecular evolution of the Rubisco large (L-) subunit in 78 orchids and 144 bromeliads with C3 and CAM photosynthetic pathways. The sequence analyses were complemented with measurements of Rubisco kinetics in some species with contrasting photosynthetic mechanism and differing in the L-subunit sequence. Results: We identified potential positively selected sites and residues with signatures of co-adaptation. The implementation of a decision tree model related Rubisco specific variable sites to the leaf carbon isotopic composition of the species. Differences in the Rubisco catalytic traits found among C3 orchids and between strong CAM and C3 bromeliads suggested Rubisco had evolved in response to differing CO2 concentration. Conclusions: The results revealed that the variability in the Rubisco L-subunit sequence in orchids and bromeliads is composed of coevolving sites under potential positive adaptive signal. The sequence variability was related to δ13C in orchids and bromeliads, however it could not be linked to the variability found in the kinetic properties of the studied species