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07 Sep 2021
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The origin of the allometric scaling of lung ventilation in mammals

How mammals adapt their breath to body activity – and how this depends on body size

Recommended by ORCID_LOGO based on reviews by Elad Noor, Oliver Ebenhöh, Stefan Schuster and Megumi Inoue

How fast and how deep do animals breathe, and how does this depend on how active they are? To answer this question, one needs to dig deeply into how breathing works and what biophysical processes it involves. And one needs to think about body size.

It is impressive how nature adapts the same body plan – e.g. the skeletal structure of mammals – to various shapes and sizes. From mice to whales, also the functioning of most organs remains the same; they are just differently scaled. Scaling does not just mean “making bigger or smaller”. As already noted by Galilei, body shapes change as they are adapted to body dimensions, and the same holds for physiological variables. Many such variables, for instance, heartbeat rates, follow scaling laws of the form y~x^a, where x denotes body mass and the exponent a is typically a multiple of ¼ [1]. These unusual exponents – instead of multiples of ⅓, which would be expected from simple geometrical scaling – are why these laws are called “allometric”. Kleiber’s law for metabolic rates, with a scaling exponent of ¾, is a classic example [2]. As shown by G. West, allometric laws can be explained through a few simple steps [1]. In his models, he focused on network-like organs such as the vascular system and assumed that these systems show a self-similar structure, with a fixed minimal unit (for instance, capillaries) but varying numbers of hierarchy levels depending on body size. To determine the flow through such networks, he employed biophysical models and optimality principles (for instance, assuming that oxygen must be transported at a minimal mechanical effort), and showed that the solutions – and the physiological variables – respect the known scaling relations.

The paper “The origin of the allometric scaling of lung ventilation in mammals“ by Noël et al. [3], applies this thinking to the depth and rate of breathing in mammals. Scaling laws describing breathing in resting animals have been known since the 1950s [4], with exponents of 1 (for tidal volume) and -¼ (for breathing frequency). Equipped with a detailed biophysical model, Noël et al. revisit this question, extending these laws to other metabolic regimes. Their starting point is a model of the human lung, developed previously by two of the authors [5], which assumes that we meet our oxygen demand with minimal lung movements. To state this as an optimization problem, the model combines two submodels: a mechanical model describing the energetic effort of ventilation and a highly detailed model of convection and diffusion in self-similar lung geometries. Breathing depths and rates are computed by numerical optimization, and to obtain results for mammals of any size many of the model parameters are described by known scaling laws. As expected, the depth of breathing (measured by tidal volume) scales almost proportionally with body mass and increases with metabolic demand, while the breathing rate decreases with body mass, with an exponent of about -¼. However, the laws for the breathing rate hold only for basal activity; at higher metabolic rates, which are modeled here for the first time, the exponent deviates strongly from this value, in line with empirical data.

Why is this paper important? The authors present a highly complex model of lung physiology that integrates a wide range of biophysical details and passes a difficult test: the successful prediction of unexplained scaling exponents. These scaling relations may help us transfer insights from animal models to humans and in reverse: data for breathing during exercise, which are easy to measure in humans, can be extrapolated to other species. Aside from the scaling laws, the model also reveals physiological mechanisms. In the larger lung branches, oxygen is transported mainly by air movement (convection), while in smaller branches air flow is slow and oxygen moves by diffusion. The transition between these regimes can occur at different depths in the lung: as the authors state, “the localization of this transition determines how ventilation should be controlled to minimize its energetic cost at any metabolic regime”. In the model, the optimal location for the transition depends on oxygen demand [5, 6]: the transition occurs deeper in the lung in exercise regimes than at rest, allowing for more oxygen to be taken up. However, the effects of this shift depend on body size: while small mammals generally use the entire exchange surface of their lungs, large mammals keep a reserve for higher activities, which becomes accessible as their transition zone moves at high metabolic rates. Hence, scaling can entail qualitative differences between species!

Altogether, the paper shows how the dynamics of ventilation depend on lung morphology. But this may also play out in the other direction: if energy-efficient ventilation depends on body activity, and therefore on ecological niches, a niche may put evolutionary pressures on lung geometry. Hence, by understanding how deep and fast animals breathe, we may also learn about how behavior, physiology, and anatomy co-evolve.

References

[1] West GB, Brown JH, Enquist BJ (1997) A General Model for the Origin of Allometric Scaling Laws in Biology. Science 276 (5309), 122–126. https://doi.org/10.1126/science.276.5309.122

[2] Kleiber M (1947) Body size and metabolic rate. Physiological Reviews, 27, 511–541. https://doi.org/10.1152/physrev.1947.27.4.511

[3] Noël F., Karamaoun C., Dempsey J. A. and Mauroy B. (2021) The origin of the allometric scaling of lung's ventilation in mammals. arXiv, 2005.12362, ver. 6 peer-reviewed and recommended by Peer community in Mathematical and Computational Biology. https://arxiv.org/abs/2005.12362

[4] Otis AB, Fenn WO, Rahn H (1950) Mechanics of Breathing in Man. Journal of Applied Physiology, 2, 592–607. https://doi.org/10.1152/jappl.1950.2.11.592

[5] Noël F, Mauroy B (2019) Interplay Between Optimal Ventilation and Gas Transport in a Model of the Human Lung. Frontiers in Physiology, 10, 488. https://doi.org/10.3389/fphys.2019.00488

[6] Sapoval B, Filoche M, Weibel ER (2002) Smaller is better—but not too small: A physical scale for the design of the mammalian pulmonary acinus. Proceedings of the National Academy of Sciences, 99, 10411–10416. https://doi.org/10.1073/pnas.122352499

The origin of the allometric scaling of lung ventilation in mammalsFrédérique Noël, Cyril Karamaoun, Jerome A. Dempsey, Benjamin Mauroy<p>A model of optimal control of ventilation has recently been developed for humans. This model highlights the importance of the localization of the transition between a convective and a diffusive transport of respiratory gas. This localization de...Biophysics, Evolutionary Biology, PhysiologyWolfram Liebermeister2020-08-28 15:18:03 View
26 Feb 2024
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A workflow for processing global datasets: application to intercropping

Collecting, assembling and sharing data in crop sciences

Recommended by ORCID_LOGO based on reviews by Christine Dillmann and 2 anonymous reviewers

It is often the case that scientific knowledge exists but is scattered across numerous experimental studies. Because of this dispersion in different formats, it remains difficult to access, extract, reproduce, confirm or generalise. This is the case in crop science, where Mahmoud et al [1] propose to collect and assemble data from numerous field experiments on intercropping.

It happens that the construction of the global dataset requires a lot of time, attention and a well thought-out method, inspired by the literature on data science [2] and adapted to the specificities of crop science. This activity also leads to new possibilities that were not available in individual datasets, such as the detection of full factorial designs using graph theory tools developed on top of the global dataset.

The study by Mahmoud et al [1] has thus multiple dimensions:

  • The description of the solutions given to this data assembly challenge.
  • The illustration of the usefulness of such procedure in a case study of 37 field experiments on cereal-legume associations. The dataset is publicly available [3], while some results obtained from it have been independently published elsewhere [e.g. 4].
  • The description of an algorithm able to detect complete factorial designs.
  • An informed discussion of the merits of global datasets compared to alternatives, in particular meta-analyses
  • A documented reflection on scientific practices in the era of big data, guided by the principles of open science.

I was particularly interested in the promotion of the FAIR principles, perhaps used a little too uncritically in my view, as an obvious solution to data sharing. On the one hand, I am admiring and grateful for the availability of these data, some of which have never been published, nor associated with published results. This approach is likely to unearth buried treasures. On the other hand, I can understand the reluctance of some data producers to commit to total, definitive sharing, facilitating automatic reading, without having thought about a certain reciprocity on the part of users and use by artificial intelligence. Reciprocity in terms of recognition, as is discussed by Mahmoud et al [1], but also in terms of contribution to the commons [5] or reading conditions for machine learning.
But this is another subject, to be dealt with in the years to come, and for which, perhaps, the contribution recommended here will be enlightening.

References

[1] Mahmoud R., Casadebaig P., Hilgert N., Gaudio N. A workflow for processing global datasets: application to intercropping. 2024. ⟨hal-04145269v2⟩ ver. 2 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://hal.science/hal-04145269

[2] Wickham, H. 2014. Tidy data. Journal of Statistical Software 59(10) https://doi.org/10.18637/jss.v059.i10

[3] Gaudio, N., R. Mahmoud, L. Bedoussac, E. Justes, E.-P. Journet, et al. 2023. A global dataset gathering 37 field experiments involving cereal-legume intercrops and their corresponding sole crops. https://doi.org/10.5281/zenodo.8081577

[4] Mahmoud, R., Casadebaig, P., Hilgert, N. et al. Species choice and N fertilization influence yield gains through complementarity and selection effects in cereal-legume intercrops. Agron. Sustain. Dev. 42, 12 (2022). https://doi.org/10.1007/s13593-022-00754-y

[5] Bernault, C. « Licences réciproques » et droit d'auteur : l'économie collaborative au service des biens communs ?. Mélanges en l'honneur de François Collart Dutilleul, Dalloz, pp.91-102, 2017, 978-2-247-17057-9. https://shs.hal.science/halshs-01562241

A workflow for processing global datasets: application to intercroppingRémi Mahmoud, Pierre Casadebaig, Nadine Hilgert, Noémie Gaudio<p>Field experiments are a key source of data and knowledge in agricultural research. An emerging practice is to compile the measurements and results of these experiments (rather than the results of publications, as in meta-analysis) into global d...Agricultural ScienceEric Tannier2023-06-29 15:38:28 View
10 Jan 2024
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An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla

Aphid: A Novel Statistical Method for Dissecting Gene Flow and Lineage Sorting in Phylogenetic Conflict

Recommended by ORCID_LOGO based on reviews by Richard Durbin and 2 anonymous reviewers

Galtier [1] introduces “Aphid,” a new statistical method that estimates the contributions of gene flow (GF) and incomplete lineage sorting (ILS) to phylogenetic conflict.  Aphid is based on the observation that GF tends to make gene genealogies shorter, whereas ILS makes them longer.  Rather than fitting the full likelihood, it models the distribution of gene genealogies as a mixture of several canonical gene genealogies in which coalescence times are set equal to their expectations under different models. This simplification makes Aphid far faster than competing methods. In addition, it deals gracefully with bidirectional gene flow—an impossibility under competing models. Because of these advantages, Aphid represents an important addition to the toolkit of evolutionary genetics.

In the interest of speed, Aphid makes several simplifying assumptions. Yet even when these were violated, Aphid did well at estimating parameters from simulated data. It seems to be reasonably robust.

Aphid studies phylogenetic conflict, which occurs when some loci imply one phylogenetic tree and other loci imply another. This happens when the interval between successive speciation events is fairly short. If this interval is too short,  however,  Aphid’s approximations break down, and its estimates are biased. Galtier suggests caution when the fraction of discordant phylogenetic trees exceeds 50–55%. Thus, Aphids will be most useful when the interval between speciation events is short, but not too short.

Galtier applies the new method to three sets of primate data. In two of these data sets  (baboons and African apes), Aphid detects gene flow that would likely be missed by competing methods. These competing methods are primarily sensitive to gene flow that is asymmetric in two senses: (1) greater flow in one direction than the other, and (2) unequal gene flow connecting an outgroup to two sister species.  Aphid finds evidence of symmetric gene flow in the ancestry of baboons and also in that of African apes. The data suggest that ancestral humans and chimpanzees both interbred with ancestral gorillas, and at about the same rate.  Aphid’s ability to detect this signature sets it apart from competing methods.

References

[1]   Nicolas Galtier (2023) “An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorilla”. bioRxiv, ver. 3 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology.  https://doi.org/10.1101/2023.07.06.547897

An approximate likelihood method reveals ancient gene flow between human, chimpanzee and gorillaNicolas Galtier<p>Gene flow and incomplete lineage sorting are two distinct sources of phylogenetic conflict, i.e., gene trees that differ in topology from each other and from the species tree. Distinguishing between the two processes is a key objective of curre...Evolutionary Biology, Genetics and population Genetics, Genomics and TranscriptomicsAlan Rogers2023-07-06 18:41:16 View
24 Dec 2020
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A linear time solution to the Labeled Robinson-Foulds Distance problem

Comparing reconciled gene trees in linear time

Recommended by ORCID_LOGO based on reviews by Barbara Holland, Gabriel Cardona, Jean-Baka Domelevo Entfellner and 1 anonymous reviewer

Unlike a species tree, a gene tree results not only from speciation events, but also from events acting at the gene level, such as duplications and losses of gene copies, and gene transfer events [1]. The reconciliation of phylogenetic trees consists in embedding a given gene tree into a known species tree and, doing so, determining the location of these gene-level events on the gene tree [2]. Reconciled gene trees can be seen as phylogenetic trees where internal node labels are used to discriminate between different gene-level events. Comparing them is of foremost importance in order to assess the performance of various reconciliation methods (e.g. [3]).
A paper describing an extension of the widely used Robinson-Foulds (RF) distance [4] to trees with labeled internal nodes was presented earlier this year [5]. This distance, called ELRF, is based on edge edits and coincides with the RF distance when all internal labels are identical; unfortunately, the ELRF distance is very costly to compute. In the present paper [6], the authors introduce a distance called LRF, which is inspired by the TED (Tree Edit Distance [7]) and is based on node edits. As the ELRF, the new distance coincides with the RF distance for identically-labeled internal nodes, but has the additional desirable features of being computable in linear time. Also, in the ELRF distance, an edge can be deleted if only it connects nodes with the same label. The new formulation does not have this restriction, and this is, in my opinion, an improvement since the restriction makes little sense in the comparison of reconciled gene trees.
The authors show the pertinence of this new distance by studying the impact of taxon sampling on reconciled gene trees when internal labels are computed via a method based on species overlap. The linear algorithm to compute the LRF distance presented in the paper has been implemented and the software —written in Python— is freely available for the community to use it. I bet that the LRF distance will be widely used in the coming years!

References

[1] Maddison, W. P. (1997). Gene trees in species trees. Systematic biology, 46(3), 523-536. doi: https://doi.org/10.1093/sysbio/46.3.523
[2] Boussau, B., and Scornavacca, C. (2020). Reconciling gene trees with species trees. Phylogenetics in the Genomic Era, p. 3.2:1–3.2:23. [3] Doyon, J. P., Chauve, C., and Hamel, S. (2009). Space of gene/species trees reconciliations and parsimonious models. Journal of Computational Biology, 16(10), 1399-1418. doi: https://doi.org/10.1089/cmb.2009.0095
[4] Robinson, D. F., and Foulds, L. R. (1981). Comparison of phylogenetic trees. Mathematical biosciences, 53(1-2), 131-147. doi: https://doi.org/10.1016/0025-5564(81)90043-2
[5] Briand, B., Dessimoz, C., El-Mabrouk, N., Lafond, M. and Lobinska, G. (2020). A generalized Robinson-Foulds distance for labeled trees. BMC Genomics 21, 779. doi: https://doi.org/10.1186/s12864-020-07011-0
[6] Briand, S., Dessimoz, C., El-Mabrouk, N. and Nevers, Y. (2020) A linear time solution to the labeled Robinson-Foulds distance problem. bioRxiv, 2020.09.14.293522, ver. 4 peer-reviewed and recommended by PCI Mathematical and Computational Biology. doi: https://doi.org/10.1101/2020.09.14.293522
[7] Zhang, K., and Shasha, D. (1989). Simple fast algorithms for the editing distance between trees and related problems. SIAM journal on computing, 18(6), 1245-1262. doi: https://doi.org/10.1137/0218082

A linear time solution to the Labeled Robinson-Foulds Distance problemSamuel Briand, Christophe Dessimoz, Nadia El-Mabrouk and Yannis Nevers <p>Motivation Comparing trees is a basic task for many purposes, and especially in phylogeny where different tree reconstruction tools may lead to different trees, likely representing contradictory evolutionary information. While a large variety o...Combinatorics, Design and analysis of algorithms, Evolutionary BiologyCéline Scornavacca2020-08-20 21:06:23 View
18 Apr 2023
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Cancer phylogenetic tree inference at scale from 1000s of single cell genomes

Phylogenetic reconstruction from copy number aberration in large scale, low-depth genome-wide single-cell data.

Recommended by based on reviews by 3 anonymous reviewers

The paper [1] presents and applies a new Bayesian inference method of phylogenetic reconstruction for multiple sequence alignments in the case of low sequencing coverage but diverse copy number aberrations (CNA), with applications to single cell sequencing of tumors.

The idea is to take advantage of CNA to reconstruct the topology of the phylogenetic tree of sequenced cells in a first step (the `sitka' method), and in a second step to assign single nucleotide variants (SNV) to tree edges (and then calibrate their lengths) (the `sitka-snv' method).

The data are summarized into a binary-valued CxL matrix Y, where C is the number of cells and L is the number of loci (here, loci are segments of prescribed length called `bins'). The entry of Y at row i and column j is 1 (otherwise 0) iff in the ancestral lineage of cell i, at least one genomic rearrangement has occurred, and more specifically the gain or loss of a segment with at least one endpoint in locus j or in locus j+1. The authors expect the infinite-allele assumption to approximately hold (i.e., that at most one mutation occurs at any given marker and that 0 is the ancestral state). They refer to this assumption as the `perfect phylogeny assumption'. By only recording from CNA events the endpoints at which they occur, the authors lose the information on copy number, but they gain the assumption of independence of the mutational processes occurring at different sites, which approximately holds for CNA endpoints.

The goal of sitka is to produce a posterior distribution on phylogenetic trees conditional on the matrix Y , where here a phylogenetic tree is understood as containing the information on 1) the topology of the tree but not its edge lengths, and 2) for each edge, the identity of markers having undergone a mutation, in the sense of the previous paragraph. 

The results of the method are tested against synthetic datasets simulated under various assumptions, including conditions violating the perfect phylogeny assumption and compared to results obtained under other baseline methods. The method is extended to assign SNV to edges of the tree inferred by sitka. It is also applied to real datasets of single cell genomes of tumors. 

The manuscript is very well-written, with a high degree of detail. The method is novel, scalable, fast and appears to perform favorably compared to other approaches. It has been applied in independent publications, for example to multi-year time-series single-cell whole-genome sequencing of tumors, in order to infer the fitness landscape and its dynamics through time, see [2].

The reviewing process has taken too long, mainly because of other commitments I had during the period and to the difficulty of finding reviewers. Let me apologize to the authors and thank them for their patience as well as for the scientific rigor they brought to their revisions and answers to reviewers, who I also warmly thank for their quality work.

REFERENCES

[1] Sohrab Salehi, Fatemeh Dorri, Kevin Chern, Farhia Kabeer, Nicole Rusk, Tyler Funnell, Marc J Williams, Daniel Lai, Mirela Andronescu, Kieran R. Campbell, Andrew McPherson, Samuel Aparicio, Andrew Roth, Sohrab Shah, and Alexandre Bouchard-Côté. Cancer phylogenetic tree inference at scale from 1000s of single cell genomes (2023). bioRxiv, 2020.05.06.058180, ver. 4 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. 
https://doi.org/10.1101/2020.05.06.058180

[2] Sohrab Salehi, Farhia Kabeer, Nicholas Ceglia, Mirela Andronescu, Marc J. Williams, Kieran R. Campbell, Tehmina Masud, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Hakwoo Lee, Jerome Ting, Allen W. Zhang, Hoa Tran, Ciara O’Flanagan, Fatemeh Dorri, Nicole Rusk, Teresa Ruiz de Algara, So Ra Lee, Brian Yu Chieh Cheng, Peter Eirew, Takako Kono, Jenifer Pham, Diljot Grewal, Daniel Lai, Richard Moore, Andrew J. Mungall, Marco A. Marra, IMAXT Consortium, Andrew McPherson, Alexandre Bouchard-Côté, Samuel Aparicio & Sohrab P. Shah. Clonal fitness inferred from time-series modelling of single-cell cancer genomes (2021).  Nature 595, 585–590. https://doi.org/10.1038/s41586-021-03648-3

Cancer phylogenetic tree inference at scale from 1000s of single cell genomesSohrab Salehi, Fatemeh Dorri, Kevin Chern, Farhia Kabeer, Nicole Rusk, Tyler Funnell, Marc J Williams, Daniel Lai, Mirela Andronescu, Kieran R. Campbell, Andrew McPherson, Samuel Aparicio, Andrew Roth, Sohrab Shah, and Alexandre Bouchard-Côté<p style="text-align: justify;">A new generation of scalable single cell whole genome sequencing (scWGS) methods allows unprecedented high resolution measurement of the evolutionary dynamics of cancer cell populations. Phylogenetic reconstruction ...Evolutionary Biology, Genetics and population Genetics, Genomics and Transcriptomics, Machine learning, Probability and statisticsAmaury Lambert2021-12-10 17:08:04 View
13 Dec 2021
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Within-host evolutionary dynamics of antimicrobial quantitative resistance

Modelling within-host evolutionary dynamics of antimicrobial resistance

Recommended by based on reviews by 2 anonymous reviewers

Antimicrobial resistance (AMR) arises due to two main reasons: pathogens are either intrinsically resistant to the antimicrobials, or they can develop new resistance mechanisms in a continuous fashion over time and space. The latter has been referred to as within-host evolution of antimicrobial resistance and studied in infectious disease settings such as Tuberculosis [1]. During antibiotic treatment for example within-host evolutionary AMR dynamics plays an important role [2] and presents significant challenges in terms of optimizing treatment dosage. The study by Djidjou-Demasse et al. [3] contributes to addressing such challenges by developing a modelling approach that utilizes integro-differential equations to mathematically capture continuity in the space of the bacterial resistance levels.

Given its importance as a major public health concern with enormous societal consequences around the world, the evolution of drug resistance in the context of various pathogens has been extensively studied using population genetics approaches [4]. This problem has been also addressed using mathematical modelling approaches including Ordinary Differential Equations (ODE)-based [5. 6] and more recently Stochastic Differential Equations (SDE)-based models [7]. In [3] the authors propose a model of within-host AMR evolution in the absence and presence of drug treatment. The advantage of the proposed modelling approach is that it allows for AMR to be represented as a continuous quantitative trait, describing the level of resistance of the bacterial population termed quantitative AMR (qAMR) in [3]. Moreover, consistent with recent experimental evidence [2] integro-differential equations take into account both, the dynamics of the bacterial population density, referred to as “bottleneck size” in [2] as well as the evolution of its level of resistance due to drug-induced selection. 

The model proposed in [3] has been extensively and rigorously analysed to address various scenarios including the significance of host immune response in drug efficiency, treatment failure and preventive strategies. The drug treatment chosen to be investigated in this study, namely chemotherapy, has been characterised in terms of the level of evolved resistance by the bacterial population in presence of antimicrobial pressure at equilibrium.

Furthermore, the minimal duration of drug administration on bacterial growth and the emergence of AMR has been probed in the model by changing the initial population size and average resistance levels. A potential limitation of the proposed model is the assumption that mutations occur frequently (i.e. during growth), which may not be necessarily the case in certain experimental and/or clinical situations.

References

[1] Castro RAD, Borrell S, Gagneux S (2021) The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiology Reviews, 45, fuaa071. https://doi.org/10.1093/femsre/fuaa071

[2] Mahrt N, Tietze A, Künzel S, Franzenburg S, Barbosa C, Jansen G, Schulenburg H (2021) Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance. Nature Ecology & Evolution, 5, 1233–1242. https://doi.org/10.1038/s41559-021-01511-2

[3] Djidjou-Demasse R, Sofonea MT, Choisy M, Alizon S (2021) Within-host evolutionary dynamics of antimicrobial quantitative resistance. HAL, hal-03194023, ver. 4 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://hal.archives-ouvertes.fr/hal-03194023

[4] Wilson BA, Garud NR, Feder AF, Assaf ZJ, Pennings PS (2016) The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens. Molecular Ecology, 25, 42–66. https://doi.org/10.1111/mec.13474

[5] Blanquart F, Lehtinen S, Lipsitch M, Fraser C (2018) The evolution of antibiotic resistance in a structured host population. Journal of The Royal Society Interface, 15, 20180040. https://doi.org/10.1098/rsif.2018.0040

[6] Jacopin E, Lehtinen S, Débarre F, Blanquart F (2020) Factors favouring the evolution of multidrug resistance in bacteria. Journal of The Royal Society Interface, 17, 20200105. https://doi.org/10.1098/rsif.2020.0105

[7] Igler C, Rolff J, Regoes R (2021) Multi-step vs. single-step resistance evolution under different drugs, pharmacokinetics, and treatment regimens (BS Cooper, PJ Wittkopp, Eds,). eLife, 10, e64116. https://doi.org/10.7554/eLife.64116

Within-host evolutionary dynamics of antimicrobial quantitative resistanceRamsès Djidjou-Demasse, Mircea T. Sofonea, Marc Choisy, Samuel Alizon<p style="text-align: justify;">Antimicrobial efficacy is traditionally described by a single value, the minimal inhibitory concentration (MIC), which is the lowest concentration that prevents visible growth of the bacterial population. As a conse...Dynamical systems, Epidemiology, Evolutionary Biology, Medical SciencesKrasimira Tsaneva2021-04-16 16:55:19 View
14 Mar 2023
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Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis

Reprogramming of locally-monotone Boolean networks with BoNesis

Recommended by based on reviews by Ismail Belgacem and 1 anonymous reviewer

Reprogramming of cellular networks is a well known challenge in computational biology consisting first of all in properly representing an ensemble of networks having a role in a phenomenon of interest, and secondly in designing strategies to alter the functioning of this ensemble in the desired direction.  Important applications involve disease study: a therapy can be seen as a reprogramming strategy, and the disease itself can be considered a result of a series of adversarial reprogramming actions.  The origins of this domain go back to the seminal paper by Barabási et al. [1] which formalized the concept of network medicine.

An abstract tool which has gathered considerable success in network medicine and network biology are Boolean networks: sets of Boolean variables, each equipped with a Boolean update function describing how to compute the next value of the variable from the values of the other variables.  Despite apparent dissimilarity with the biological systems which involve varying quantities and continuous processes, Boolean networks have been very effective in representing biological networks whose entities are typically seen as being on or off.  Particular examples are protein signalling networks as well as gene regulatory networks.

The paper [2] by Loïc Paulevé presents a versatile tool for tackling reprogramming of Boolean networks seen as models of biological networks.  The problem of reprogramming is often formulated as the problem of finding a set of perturbations which guarantee some properties on the attractors.  The work [2] relies on the most permissive semantics [3], which together with the modelling assumption allows for considerable speed-up in the practically relevant subclass of locally-monotone Boolean networks.

The paper is structured as a tutorial.  It starts by introducing the formalism, defining 4 different general variants of reprogramming under the most permissive semantics, and presenting evaluations of their complexity in terms of the polynomial hierarchy.  The author then describes the software tool BoNesis which can handle different problems related to Boolean networks, and in particular the 4 reprogramming variants.  The presentation includes concrete code examples with their output, which should be very helpful for future users.

The paper [2] introduces a novel scenario: reprogramming of ensembles of Boolean networks delineated by some properties, including for example the property of having a given interaction graph.  Ensemble reprogramming looks particularly promising in situations in which the biological knowledge is insufficient to fully determine all the update functions, i.e. in the majority of modelling situations.  Finally, the author also shows how BoNesis can be used to deal with sequential reprogramming, which is another promising direction in computational controllability, potentially enabling more efficient therapies [4,5].

REFERENCES
  1. Barabási A-L, Gulbahce N, Loscalzo J (2011) Network medicine: a network-based approach to human disease. Nature Reviews Genetics, 12, 56–68. https://doi.org/10.1038/nrg2918
  2. Paulevé L (2023) Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis. arXiv, ver. 2 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.48550/arXiv.2207.13307
  3. Paulevé L, Kolčák J, Chatain T, Haar S (2020) Reconciling qualitative, abstract, and scalable modeling of biological networks. Nature Communications, 11, 4256. https://doi.org/10.1038/s41467-020-18112-5
  4. Mandon H, Su C, Pang J, Paul S, Haar S, Paulevé L (2019) Algorithms for the Sequential Reprogramming of Boolean Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 1610–1619. https://doi.org/10.1109/TCBB.2019.2914383
  5. Pardo J, Ivanov S, Delaplace F (2021) Sequential reprogramming of biological network fate. Theoretical Computer Science, 872, 97–116. https://doi.org/10.1016/j.tcs.2021.03.013
Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesisLoïc Paulevé<p style="text-align: justify;">Boolean networks (BNs) are discrete dynamical systems with applications to the modeling of cellular behaviors. In this paper, we demonstrate how the software BoNesis can be employed to exhaustively identify combinat...Combinatorics, Computational complexity, Dynamical systems, Molecular Biology, Systems biologySergiu Ivanov Ismail Belgacem, Anonymous2022-08-31 15:00:21 View
09 Nov 2023
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A mechanistic-statistical approach to infer dispersal and demography from invasion dynamics, applied to a plant pathogen

A mechanistic-statistical approach for the field-based study of invasion dynamics

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

​To study the annual invasion of a tree pathogen (Melampsora larici-populina, a fungal species responsible for the poplar rust disease), Xhaard et al (2012) had conducted a spatiotemporal survey along the Durance River valley in the French Alps over nearly 200 km, measuring sampled leaves and twigs from 40 to 150 trees at 12 evenly spaced study sites at seven-time points. By combining Bayesian genetic assignment and a landscape epidemiology approach, they were able to estimate the genetic origin and annual spread of the plant pathogen during a single epidemic.

The observed temporal variation in the spatial pattern of infection rates allowed Saubin et al (2023) to estimate the key factors that determine the speed of the invasion dynamics. In particular, it is crucial to estimate the probability and extent of long-distance dispersal. The dynamics of the macroscale population density was formulated by the reaction-diffusion (R.D.) model and by the integro-difference (I.D.) model. Both consist of the diffusion/dispersal component and the reaction component. In the I.D. model, the kernel function represents the distribution of the dispersion. The likelihood function was obtained by coupling the mathematical model of the population dynamics and the statistical model of the observational process.

Saubin et al (2023) considered a thin-tailed Gaussian kernel, a heavy-tailed exponential kernel, and a fat-tailed exponential power kernel. The numerical simulation reflecting the above survey confirmed the identifiability of the propagation kernel and the accuracy of the parameter estimation. In particular, the above survey had the high power to identify the model with frequent long-distance dispersal. The data from the survey selected the exponential power kernel with confidence. The mean dispersal distance was estimated to be 2.01 km. The exponential power was 0.24. This parameter value predicts that 5% of the dispersals will have a distance > 14.3 km and 1% will have a distance > 36.0 km. The mechanistic-statistical approach presented here may become a new standard for the field-based studies of invasion dynamics.

References

Saubin, M., Coville, J., Xhaard, C., Frey, P., Soubeyrand, S., Halkett, F., and Fabre, F. (2023). A mechanistic-statistical approach to infer dispersal and demography from invasion dynamics, applied to a plant pathogen. bioRxiv, ver. 5 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2023.03.21.533642

Xhaard, C., Barrès, B., Andrieux, A., Bousset, L., Halkett, F., and Frey, P. (2012). Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Molecular Ecology, 21(10):2383-2398. https://doi.org/10.1111/j.1365-294X.2012.05556.x

A mechanistic-statistical approach to infer dispersal and demography from invasion dynamics, applied to a plant pathogenMéline Saubin, Jérome Coville, Constance Xhaard, Pascal Frey, Samuel Soubeyrand, Fabien Halkett, Frédéric Fabre<p style="text-align: justify;">Dispersal, and in particular the frequency of long-distance dispersal (LDD) events, has strong implications for population dynamics with possibly the acceleration of the colonisation front, and for evolution with po...Dynamical systems, Ecology, Epidemiology, Probability and statisticsHirohisa Kishino2023-05-10 09:57:25 View
27 Jul 2021
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Estimating dates of origin and end of COVID-19 epidemics

The importance of model assumptions in estimating the dynamics of the COVID-19 epidemic

Recommended by based on reviews by Bastien Boussau and 1 anonymous reviewer

In “Estimating dates of origin and end of COVID-19 epidemics”, Bénéteau et al. develop and apply a mathematical modeling approach to estimate the date of the origin of the SARS-CoV-2 epidemic in France. They also assess how long strict control measures need to last to ensure that the prevalence of the virus remains below key public health thresholds. This problem is challenging because the numbers of infected individuals in both tails of the epidemic are low, which can lead to errors when deterministic models are used. To achieve their goals, the authors developed a discrete stochastic model. The model is non-Markovian, meaning that individual infection histories influence the dynamics. The model also accounts for heterogeneity in the timing between infection and transmission and includes stochasticity as well as consideration of superspreader events. By comparing the outputs of their model with several alternative models, Bénéteau et al. were able to assess the importance of stochasticity, individual heterogeneity, and non-Markovian effects on the estimates of the dates of origin and end of the epidemic, using France as a test case. Some limitations of the study, which the authors acknowledge, are that the time from infection to death remains largely unknown, a lack of data on the heterogeneity of transmission among individuals, and the assumption that only a single infected individual caused the epidemic. Despite the acknowledged limitations of the work, the results suggest that cases may be detected long before the detection of an epidemic wave. Also, the approach may be helpful for informing public health decisions such as the necessary duration of strict lockdowns and for assessing the risks of epidemic rebound as restrictions are lifted. In particular, the authors found that estimates of the end of the epidemic following lockdowns are more sensitive to the assumptions of the models used than estimates of its beginning. In summary, this model adds to a valuable suite of tools to support decision-making in response to disease epidemics.

References

Bénéteau T, Elie B, Sofonea MT, Alizon S (2021) Estimating dates of origin and end of COVID-19 epidemics. medRxiv, 2021.01.19.21250080, ver. 3 peer-reviewed and recommended by Peer Community in Mathematical and Computational Biology. https://doi.org/10.1101/2021.01.19.21250080

Estimating dates of origin and end of COVID-19 epidemicsThomas Bénéteau, Baptiste Elie, Mircea T. Sofonea, Samuel Alizon<p style="text-align: justify;">Estimating the date at which an epidemic started in a country and the date at which it can end depending on interventions intensity are important to guide public health responses. Both are potentially shaped by simi...Epidemiology, Probability and statistics, Stochastic dynamicsValery Forbes2021-02-23 16:37:32 View
12 Oct 2023
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When Three Trees Go to War

Bounding the reticulation number for three phylogenetic trees

Recommended by based on reviews by Guillaume Scholz and Stefan Grünewald

Reconstructing a phylogenetic network for a set of conflicting phylogenetic trees on the same set of leaves remains an active strand of research in mathematical and computational phylogenetic since 2005, when Baroni et al. [1] showed that the minimum number of reticulations h(T,T') needed to simultaneously embed two rooted binary phylogenetic trees T and T' into a rooted binary phylogenetic network is one less than the size of a maximum acyclic agreement forest for T and T'. In the same paper, the authors showed that h(T,T') is bounded from above by n-2, where n is the number of leaves of T and T' and that this bound is sharp. That is, for a fixed n, there exist two rooted binary phylogenetic trees T and T' such that h(T,T')=n-2.

Since 2005, many papers have been published that develop exact algorithms and heuristics to solve the above NP-hard minimisation problem in practice, which is often referred to as Minimum Hybridisation in the literature, and that further investigate the mathematical underpinnings of Minimum Hybridisation and related problems. However, many such studies are restricted to two trees and much less is known about Minimum Hybridisation for when the input consists of more than two phylogenetic trees, which is the more relevant cases from a biological point of view. 

In [2], van Iersel, Jones, and Weller establish the first lower bound for the minimum reticulation number for more than two rooted binary phylogenetic trees, with a focus on exactly three trees. The above-mentioned connection between the minimum number of reticulations and maximum acyclic agreement forests does not extend to three (or more) trees. Instead, to establish their result, the authors use multi-labelled trees as an intermediate structure between phylogenetic trees and phylogenetic networks to show that, for each ε>0, there exist three caterpillar trees on n leaves such that any phylogenetic network that simultaneously embeds these three trees has at least (3/2 - ε)n reticulations. Perhaps unsurprising, caterpillar trees were also used by Baroni et al. [1] to establish that their upper bound on h(T,T') is sharp. Structurally, these trees have the property that each internal vertex is adjacent to a leaf. Each caterpillar tree can therefore be viewed as a sequence of characters, and it is exactly this viewpoint that is heavily used in [2]. More specifically, sequences with short common subsequences correspond to caterpillar trees that need many reticulations when embedded in a phylogenetic network. It would consequently be interesting to further investigate connections between caterpillar trees and certain types of sequences. Can they be used to shed more light on bounds for the minimum reticulation number?

References

[1] Baroni, M., Grünewald, S., Moulton, V., and Semple, C. (2005) "Bounding the number of hybridisation events for a consistent evolutionary history". J. Math. Biol. 51, 171–182. https://doi.org/10.1007/s00285-005-0315-9
  
[2] van Iersel, L., Jones, M., and Weller, M. (2023) “When three trees go to war”. HAL, ver. 3 peer-reviewed and recommended by Peer Community In Mathematical and Computational Biology. https://hal.science/hal-04013152/

When Three Trees Go to War Leo van Iersel and Mark Jones and Mathias Weller<p style="text-align: justify;">How many reticulations are needed for a phylogenetic network to display a given set of k phylogenetic trees on n leaves? For k = 2, Baroni, Semple, and Steel [Ann. Comb. 8, 391-408 (2005)] showed that the answer is ...Combinatorics, Evolutionary Biology, Graph theorySimone Linz2023-03-07 18:49:21 View