A consistent least-squares criterion for calibrating edge lengths in phylogenetic networks

Jingcheng Xu; Cécile Ané

Home/Archive/arXiv

arXiv · 2407.19343

A consistent least-squares criterion for calibrating edge lengths in phylogenetic networks

Jingcheng Xu·Cécile Ané

View original source ↗Read source document ↗Export metadata ↓

Abstract

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length estimates from genetic distances, in the presence of rate variation across genes and lineages, when the network topology is known. We propose a novel criterion based on least-squares that is both consistent and computationally tractable. The crux of our approach is to decompose the genetic distances into two parts, one of which is invariant across displayed trees of the network. The scaled genetic distances are then fitted to the invariant part, while the average scaled genetic distances are fitted to the non-invariant part. We show that this criterion is consistent provided that there exists a tree path between some pair of tips in the network, and that edge lengths in the network are identifiable from average distances. We also provide a constrained variant of this criterion assuming a molecular clock, which can be used to obtain relative edge lengths in calendar time.

Explore related subjects

q-bio.PE

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Jingcheng Xu, Cécile Ané. 2024-07-27. A consistent least-squares criterion for calibrating edge lengths in phylogenetic networks. https://arxiv.org/abs/2407.19343

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

KEEP EXPLORING

Related papers

arXiv2026

Competition drives excessive recruitment in collective search

Groups that search collectively often exploit what they find by recruiting: one member directs others to a site it has found. Recruitment raises the number of members foraging at a known site, but the return per forager may fall as that number grows, so there is an intermediate optimal recruitment rate. In addition, a site may be used by more than one group. Here we analyze a model of two groups that forage from a single site whose return declines with the total number of foragers present. The two groups interact only through this shared return. The long-run outcome is either coexistence at the foraging site or monopoly by one group, and we analyze the boundary between these two outcomes. A group's best response to its rival is not monotone: it increases its own recruitment rate with the rival's recruitment rate in an attempt to preserve a monopoly, and then its recruitment rate drops discontinuously when it is no longer optimal to preserve a monopoly. We analyze how model parameters govern this shift: a group relinquishes monopoly when the site saturates at few foragers and when the rival group is small. When the two groups have comparable size there are multiple Nash equilibria, so either group may end up with the larger share. And when two equally matched groups compete, both recruit above the rate that maximizes their common return, so that each individual ends with less than it would in a single undivided group of the same total size.

q-bio.PE↗

arXiv2026

Selection Rules for Species Coexistence in a Hierarchical May-Leonard Model

One of the central challenges in evolutionary dynamics is understanding why some species combinations persist while others disappear. Although cyclic-interaction models have provided fundamental insights into biodiversity maintenance, much less is known about how hierarchical competitive interactions shape long-term community organization. Here, we investigate a hierarchical extension of the May-Leonard model, in which species interact through a directed predation chain while undergoing reproduction and mortality. Combining mean-field analysis with Monte Carlo simulations, we show that the fully coexisting state is generically unstable, causing the dynamics to evolve toward lower-dimensional coexistence states. The simulations further reveal stochastic extinctions dominating small populations with the dynamics progressively approaching the mean-field predictions as the system size increases. Rather than permitting arbitrary species combinations, the hierarchical-interaction structure dynamically constrains coexistence by selecting only specific subsets of species for long-term persistence. We show that these admissible coexistence states have a natural graph-theoretic interpretation as independent sets in the hierarchical interaction network, thereby providing general constraints on coexistence in hierarchical communities. Together, these results establish a theoretical framework linking hierarchical interactions, dynamical selection, graph topology, and biodiversity organization, extending the classical May-Leonard model beyond cyclic competition.

q-bio.PE↗

arXiv2026

Persistence of n-Species Lotka-Volterra Models with Periodic Pulses

Periodic impulsive interventions arise naturally in the management of biological populations, including chemotherapy, pesticide application, and infectious-disease treatment. We develop general conditions for permanence in n-species population models subject to periodic multiplicative pulse disturbances. Our main result provides a sufficient condition for permanence in terms of weighted long-term growth rates on a Morse decomposition of the extinction set, explicitly separating the contributions of continuous population dynamics from those of the periodic pulse. To establish this result, we transform the impulsive system into an associated autonomous continuous-time dynamical system and use this correspondence to extend classical permanence theory to periodically pulsed models. We further show that the same conditions imply robust permanence under sufficiently small perturbations to the continuous dynamics, pulse period, and pulse effects. We illustrate the framework with two Lotka-Volterra models motivated by biological control: competition between chemotherapy-sensitive and chemotherapy-resistant cancer cells, and integrated control of an agricultural pest using pesticides and parasitoids. These examples demonstrate how intervention frequency and intensity interact with underlying ecological interactions to determine whether populations coexist or are excluded. Our results provide a general framework for analyzing persistence in ecological systems subject to repeated discrete disturbances.

q-bio.PE↗