Markov chain approach to the distribution of ancestors in species of biparental reproduction

We studied how to obtain a distribution for the number of ancestors in species of sexual reproduction. Present models concentrate on the estimation of distributions repetitions of ancestors in genealogical trees. It has been shown that is not possible to reconstruct the genealogical history of each species along all its generations by means of a geometric progression. This analysis demonstrates that it is possible to rebuild the tree of progenitors by modeling the problem with a Markov chain. For each generation, the maximum number of possible ancestors is different. This brings huge problems for the resolution. We found a solution through a dilation of the sample space, although the distribution defined there takes smaller values respect to the initial problem. In order to correct the distribution for each generation, we introduced the invariance under gauge (local) group of dilations. These ideas can used to study the interaction of several processes and provide a new approach on the problem of the common ancestor. In the same direction, this model also provide some elements that can be used to improve models of animal reproduction.Comment: English version with change

An algorithm to represent inbreeding trees

Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees and diversity. Groups with a finite number of individuals could give a variety of genetic relationships. { In previous works \cite{PhysRevE.92.052132, PhysRevE.90.022125, JARNE20191}, we have addressed the issue of building inbreeding trees for biparental reproduction using Markovian models. Here, we extend these studies by presenting an algorithm to generate and represent inbreeding trees with no overlapping generations. We explicitly assume a two-gender reproductory scheme, and we pay particular attention to the links between nodes. We show that even for a simple case with a relatively small number of nodes in the tree, there are a large number of possible ways to rearrange the links between generations. We present an open-source python code to generate the tree graph, the adjacency matrix, and the histogram of the links for each different tree representation. We show how this mapping reflects the difference between tree realizations, and how valuable information may be extracted upon inspection of these matrices. The algorithm includes a feature to average several tree realizations, obtain the connectivity distribution, and calculate the average and mean value. We used this feature to compare trees with a different number of generations and nodes. The code presented here, available in Git-Hub, may be easily modified to be applied to other areas of interest involving connections between individuals, extend the study to add more characteristics of the different nodes, etc

Europeanization vs. Globalization? A deeper look into income and employment embodied in intra-European trade

Production processes are nowadays increasingly global, implying interdependent structures linking goods, processes and countries. Traditional economic blocks and sectoral intra-country linkages coexist with increasing worldwide dependencies. Recent literature supports the hypothesis of a new globalization process taking place in the late 1990s and the 21st century, centred on the consolidation of increasingly competitive macro-regions at a global level, with a growing specialization of countries within them. We propose a multiregional input-output (MRIO) model of the European Union (EU) to analyse whether the generation of employment and income in Europe in recent decades can be defined as a process that is mainly regional or global (involving countries within the region versus countries outside Europe). Our results show that intra-EU trade is an important factor contributing to income and employment growth, more oriented to intermediate inputs, in the same way as extra-EU trade, despite the fact that some European countries are more specialized in final goods, mainly driven by high-income EU countries. Los procesos de producción son hoy en día cada vez más globales, lo que implica estructuras interdependientes que vinculan bienes, procesos y países. Los bloques económicos tradicionales y los vínculos sectoriales dentro del país coexisten con dependencias mundiales crecientes. La literatura reciente respalda la hipótesis de un nuevo proceso de globalización que tuvo lugar a fines de los años 90 y el siglo XXI, centrado en la consolidación de macro-regiones cada vez más competitivas a nivel global, con una creciente especialización de los países dentro de ellas. Proponemos un modelo multirregional input-output (MRIO) de la Unión Europea (UE) para analizar si la generación de empleo e ingresos en Europa en las últimas décadas se puede definir como un proceso que es principalmente regional o global. Nuestros resultados muestran que el comercio intracomunitario es un factor importante que contribuye al crecimiento de los ingresos y el empleo, más orientado a los inputs intermedios, de la misma manera que el comercio extracomunitario, a pesar del hecho de que algunos países europeos están más especializados en productos finales, principalmente demandados por países de altos ingresos de la UE

Bridging gaps in the molecular phylogeny of the Lymnaeidae (Gastropoda: Pulmonata), vectors of Fascioliasis

<p>Abstract</p> <p>Background</p> <p>Lymnaeidae snails play a prominent role in the transmission of helminths, mainly trematodes of medical and veterinary importance (<it>e.g</it>., <it>Fasciola </it>liver flukes). As this family exhibits a great diversity in shell morphology but extremely homogeneous anatomical traits, the systematics of Lymnaeidae has long been controversial. Using the most complete dataset to date, we examined phylogenetic relationships among 50 taxa of this family using a supermatrix approach (concatenation of the 16 S, ITS-1 and ITS-2 genes, representing 5054 base pairs) involving both Maximum Likelihood and Bayesian Inference.</p> <p>Results</p> <p>Our phylogenetic analysis demonstrates the existence of three deep clades of Lymnaeidae representing the main geographic origin of species (America, Eurasia and the Indo-Pacific region). This phylogeny allowed us to discuss on potential biological invasions and map important characters, such as, the susceptibility to infection by <it>Fasciola hepatica </it>and <it>F. gigantica</it>, and the haploid number of chromosomes (n). We found that intermediate hosts of <it>F. gigantica </it>cluster within one deep clade, while intermediate hosts of <it>F. hepatica </it>are widely spread across the phylogeny. In addition, chromosome number seems to have evolved from n = 18 to n = 17 and n = 16.</p> <p>Conclusion</p> <p>Our study contributes to deepen our understanding of Lymnaeidae phylogeny by both sampling at worldwide scale and combining information from various genes (supermatrix approach). This phylogeny provides insights into the evolutionary relationships among genera and species and demonstrates that the nomenclature of most genera in the Lymnaeidae does not reflect evolutionary relationships. This study highlights the importance of performing basic studies in systematics to guide epidemiological control programs.</p

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers

BACKGROUND: Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries. Prior studies have demonstrated travel-related acquisition of specific opportunistic pathogens and AMR genes, but the extent and magnitude of travel\u27s effects on the gut resistome remain largely unknown. METHODS: Using whole metagenomic shotgun sequencing, functional metagenomics, and Dirichlet multinomial mixture models, we investigated the abundance, diversity, function, resistome architecture, and context of AMR genes in the fecal microbiomes of 190 Dutch individuals, before and after travel to diverse international locations. RESULTS: Travel markedly increased the abundance and α-diversity of AMR genes in the travelers\u27 gut resistome, and we determined that 56 unique AMR genes showed significant acquisition following international travel. These acquisition events were biased towards AMR genes with efflux, inactivation, and target replacement resistance mechanisms. Travel-induced shaping of the gut resistome had distinct correlations with geographical destination, so individuals returning to The Netherlands from the same destination country were more likely to have similar resistome features. Finally, we identified and detailed specific acquisition events of high-risk, mobile genetic element-associated AMR genes including qnr fluoroquinolone resistance genes, bla CONCLUSIONS: Our results show that travel shapes the architecture of the human gut resistome and results in AMR gene acquisition against a variety of antimicrobial drug classes. These broad acquisitions highlight the putative risks that international travel poses to public health by gut resistome perturbation and the global spread of locally endemic AMR genes

The Carriage of Multiresistant Bacteria after Travel (COMBAT) prospective cohort study: Methodology and design

Background: Antimicrobial resistance (AMR) is one of the major threats to public health around the world. Besides the intense use and misuse of antimicrobial agents as the major force behind the increase in antimicrobial resistance, the e

Crypto-currency bubbles: an application of the Phillips–Shi–Yu (2013) methodology on Mt. Gox bitcoin prices

The creation of bitcoin heralded the arrival of digital or crypto-currency and has been regarded as a phenomenon. Since its introduction, it has experienced a meteoric rise in price and rapid growth accompanied by huge volatility swings, and also attracted plenty of controversies which even involved law enforcement agencies. Hence, claims abound that bitcoin has been characterized by bubbles ready to burst any time (e.g. the recent collapse of bitcoin’s biggest exchange, Mt Gox). This has earned plenty of coverage in the media but surprisingly not in the academic literature. We therefore fill this knowledge gap. We conduct an econometric investigation of the existence of bubbles in the bitcoin market based on a recently developed technique that is robust in detecting bubbles – that of Phillips et al. (2013a). Over the period 2010–2014, we detected a number of short-lived bubbles; most importantly, we found three huge bubbles in the latter part of the period 2011–2013 lasting from 66 to 106 days, with the last and biggest one being the one that ‘broke the camel’s back’ – the demise of the Mt Gox exchange

The Pierre Auger Observatory III: Other Astrophysical Observations

Astrophysical observations of ultra-high-energy cosmic rays with the Pierre Auger ObservatoryComment: Contributions to the 32nd International Cosmic Ray Conference, Beijing, China, August 201

Highlights from the Pierre Auger Observatory

The Pierre Auger Observatory is the world's largest cosmic ray observatory. Our current exposure reaches nearly 40,000 km$^2$ str and provides us with an unprecedented quality data set. The performance and stability of the detectors and their enhancements are described. Data analyses have led to a number of major breakthroughs. Among these we discuss the energy spectrum and the searches for large-scale anisotropies. We present analyses of our X$_{max}$ data and show how it can be interpreted in terms of mass composition. We also describe some new analyses that extract mass sensitive parameters from the 100% duty cycle SD data. A coherent interpretation of all these recent results opens new directions. The consequences regarding the cosmic ray composition and the properties of UHECR sources are briefly discussed.Comment: 9 pages, 12 figures, talk given at the 33rd International Cosmic Ray Conference, Rio de Janeiro 201