Escape from parsimony of a double-cut-and-join genome evolution process

Mona Meghdari Miardan; Arash Jamshidpey; David Sankoff

Home/Archive/arXiv

arXiv · 2109.13424

Escape from parsimony of a double-cut-and-join genome evolution process

Mona Meghdari Miardan·Arash Jamshidpey·David Sankoff

View original source ↗Read source document ↗Export metadata ↓

Abstract

We analyze models of genome evolution based on both restricted and unrestricted double-cut-and-join (DCJ) operations. We compare the number of operations along the evolutionary trajectory to the DCJ distance of the genome from its ancestor at each step, and determine at what point they diverge: the process escapes from parsimony. Adapting the method developed by Berestycki and Durret (2006), we estimate the number of cycles in the breakpoint graph of a random genome at time $t$ and its ancestral genome by the number of tree components of an Erdös-Rényi random graph constructed from the model of evolution. In both models, the process on a genome of size $n$ is bound to its parsimonious estimate up to $t\approx n/2$ steps.

Explore related subjects

math.PR

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Mona Meghdari Miardan, Arash Jamshidpey, David Sankoff. 2021-09-28. Escape from parsimony of a double-cut-and-join genome evolution process. https://arxiv.org/abs/2109.13424

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Averaging principles for nonautonomous multiscale stochastic Burgers equations with reflection

In this paper, we study averaging principles for nonautonomous multiscale stochastic Burgers equations with reflection. First, we derive a general averaging principle applicable to such equations under minimal assumptions. Subsequently, since the coefficients of the obtained averaged equation still depend on the small scaling parameter $\e$, we impose either periodic or asymptotic conditions on the coefficients, thereby obtain two distinct averaged equations whose coefficients are independent of $\e$ and establish two averaging principles. Stopping times and Khasminskii's time discretization schemes play an important role. Finally, a concrete example is provided to illustrate the applicability and validity of the theoretical results.

math.PR↗

arXiv2026

Spectral properties of Random Matrices

We give the theoretical foundations of random matrix theory through the definitions of a random matrix, a random probability measure and the corresponding empirical spectral distribution. The technical tool we use is the Stieltjes transform method through which we prove optimal convergence of the empirical spectral distribution of random sample covariance matrices to the deterministic Marchenko-Pastur distribution. We also give new results about the rigidity of the eigenvalues of this random sample covariance matrix and the rate of their convergence. We then define the Dyson equation method to prove new local laws about a random matrix model that interpolates between the Marchenko-Pastur distribution, the elliptical law and the circular law. Through our work these local laws can be considered universal.

math.PR↗

arXiv2026

Moments approach for the elephant random walk

We discuss the method of moments for the one-dimensional elephant random walk (ERW). We first derive a differential recurrence relation for the characteristic function of the ERW, which yields a corresponding system of recurrence relations for its moments. We then obtain asymptotic approximations for the moments in each of the three parameter regimes of the ERW. Finally, by establishing the convergence of the moments and verifying the corresponding moment-determinacy conditions, we identify the limiting distributions of the ERW in each regime.

math.PR↗