arXiv subjects

C. Jarne

Publications and source records attributed to C. Jarne.

5 recordsLinked to original sources

arXiv2021

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.

q-bio.PE↗

arXiv2018

Markovian simulation for ancestors trees

We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each generation and use it to constraint the maximum number of the following generation. This new model allows to consider the reproductive preferences of particular species and combine several trees to simulate the behavior of a population. It is also possible to obtain a description analytically, considering the simulation as a theoretical stochastic process. Such process can be generalized in order to use an algorithm associated with it to simulate other similar processes of stochastic nature. The simulation is based in the theoretical model previously presented before.

q-bio.PE↗

arXiv2017

A fundamental frequency estimation method for tonal sounds inspired on bird song studies

A fast implementation of fundamental frequency estimation is presented in this work. The algorithm is based on a frequency-domain approach. It was mainly develop for tonal sounds and used in Canary bird song analysis. The method was implemented but not restricted for this kind of data. It could be easily adapted for other proposes. Python libraries were used to develop a code with a simple algorithm to obtain fundamental frequency. A simple open source code is provided in the local university repository.

cs.SD↗

arXiv2016

Equivalent Markov processes under gauge group

We have studied Markov processes on denumerable state space and continuous time. We found that all these processes are connected via gauge transformations. We have used this result before as a method for resolution of equations, included the case where the sample space is time dependent in a previous work \textit{Phys. Rev. E} \textbf{90}, 022125 (2014). We found a general solution through a dilation of the state space, although the prior probability distribution of the states defined in this new space takes smaller values with respect to the one in the initial problem. The gauge (local) group of dilations modifies the distribution on the dilated space to restore the original process. In this work we show how Markov process in general could be linked via gauge (local) transformations and we present some illustrative examples for this results.

cond-mat.stat-mech↗

arXiv2014

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.

physics.bio-ph↗