Dzunani Mthombeni, Andrew N Makanya, Sikiru Jimoh, John Maina
The developing chorioallantoic membrane (CAM) of the ostrich (Struthio camelus) was studied between embryonic days 16 (E16) and E37. Egg masses and volumes were estimated prior to harvesting of the CAM. CAM volumes were obtained before the CAM was sampled for histology and transmission electron microscopy analysis. Stereological methods were used to estimate volume densities and absolute volumes of CAM structural components. Growth rate estimates of the CAM and its major components were obtained. At E16, the three layers of the CAM were clearly delineated, but large parts still had not developed the blood-gas barrier (BGB) portions. By E37, chorionic blood capillaries had assumed a superficial position with thin BGB portions covering most of the chorionic surface. On regression analyses, the CAM had two growth phases, namely phase I that occurred between E16 and E25, when the CAM grew rapidly from a volume of 5.55 ± 1.27 to 28.82 ± 5.62 cm3 to then decrease to 25.18 ± 4.79 cm3 during phase II (E25-E37). The latter decline was attributed to changes in the chorionic and allantoic layers, while regression in the mesoderm mainly characterized blood and lymphatic vessels.This article is part of the theme issue 'The biology of the avian respiratory system'.
{"title":"A morphometric and stereological study of the chorioallantoic membrane of the developing ostrich (<i>Struthio camelus australis</i>) embryo: a light and transmission electron microscopy investigation.","authors":"Dzunani Mthombeni, Andrew N Makanya, Sikiru Jimoh, John Maina","doi":"10.1098/rstb.2023.0423","DOIUrl":"10.1098/rstb.2023.0423","url":null,"abstract":"<p><p>The developing chorioallantoic membrane (CAM) of the ostrich (<i>Struthio camelus</i>) was studied between embryonic days 16 (E16) and E37. Egg masses and volumes were estimated prior to harvesting of the CAM. CAM volumes were obtained before the CAM was sampled for histology and transmission electron microscopy analysis. Stereological methods were used to estimate volume densities and absolute volumes of CAM structural components. Growth rate estimates of the CAM and its major components were obtained. At E16, the three layers of the CAM were clearly delineated, but large parts still had not developed the blood-gas barrier (BGB) portions. By E37, chorionic blood capillaries had assumed a superficial position with thin BGB portions covering most of the chorionic surface. On regression analyses, the CAM had two growth phases, namely phase I that occurred between E16 and E25, when the CAM grew rapidly from a volume of 5.55 ± 1.27 to 28.82 ± 5.62 cm<sup>3</sup> to then decrease to 25.18 ± 4.79 cm<sup>3</sup> during phase II (E25-E37). The latter decline was attributed to changes in the chorionic and allantoic layers, while regression in the mesoderm mainly characterized blood and lymphatic vessels.This article is part of the theme issue 'The biology of the avian respiratory system'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1920","pages":"20230423"},"PeriodicalIF":5.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11864831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wonil Choi, Madeline Lazenby, Ada Forester, Haruka Wada
Global warming is one of the primary drivers of habitat loss and population decline in numerous species, including birds, amphibians and marine life. Avian embryos exhibit ectothermic phenotypes during most of their incubation period and are also vulnerable to rising temperatures when parents cannot cool the nests. This vulnerability stems from their unique respiratory mechanisms, which utilize eggshell pores to exchange respiratory gases. The number of pores is fixed at oviposition, and embryos may experience hypoxia during later developmental stages, especially when exposed to elevated ambient/incubation temperatures. Our preliminary study on zebra finch (Taeniopygia guttata castanotis) embryos, where we covered 30% of the shell surface with beeswax and incubated at high (38.9°C) temperature, revealed that half of the individuals that failed to hatch had developed oedema in the hind neck region. This study shows that such physical anomalies occur during incubation prior to death. We found that embryos with oedema had a higher head-to-body ratio, independent of their relative brain mass. Furthermore, oedema formation was correlated with darker-coloured hearts, suggesting reduced blood oxygenation in these embryos. These results highlight the physiological challenges embryos face under suboptimal incubation conditions.This article is part of the theme issue 'The biology of the avian respiratory system'.
{"title":"Respiratory challenges and oedema development in zebra finch embryos under reduced pore area.","authors":"Wonil Choi, Madeline Lazenby, Ada Forester, Haruka Wada","doi":"10.1098/rstb.2023.0436","DOIUrl":"https://doi.org/10.1098/rstb.2023.0436","url":null,"abstract":"<p><p>Global warming is one of the primary drivers of habitat loss and population decline in numerous species, including birds, amphibians and marine life. Avian embryos exhibit ectothermic phenotypes during most of their incubation period and are also vulnerable to rising temperatures when parents cannot cool the nests. This vulnerability stems from their unique respiratory mechanisms, which utilize eggshell pores to exchange respiratory gases. The number of pores is fixed at oviposition, and embryos may experience hypoxia during later developmental stages, especially when exposed to elevated ambient/incubation temperatures. Our preliminary study on zebra finch (<i>Taeniopygia guttata castanotis</i>) embryos, where we covered 30% of the shell surface with beeswax and incubated at high (38.9°C) temperature, revealed that half of the individuals that failed to hatch had developed oedema in the hind neck region. This study shows that such physical anomalies occur during incubation prior to death. We found that embryos with oedema had a higher head-to-body ratio, independent of their relative brain mass. Furthermore, oedema formation was correlated with darker-coloured hearts, suggesting reduced blood oxygenation in these embryos. These results highlight the physiological challenges embryos face under suboptimal incubation conditions.This article is part of the theme issue 'The biology of the avian respiratory system'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1920","pages":"20230436"},"PeriodicalIF":5.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0307
Emily H Dickey, Noah A Rosenberg
In mathematical models of phylogenetic trees evolving in time, a labelled history for a rooted labelled bifurcating tree is a temporal sequence of the branchings that give rise to the tree. That is, given a leaf-labelled tree with [Formula: see text] leaves and [Formula: see text] internal nodes, a labelled history is an identification between the internal nodes and the set [Formula: see text], such that the label assigned to a given node is strictly greater than the labels assigned to its descendants. We generalize the concept of labelled histories to [Formula: see text]-furcating trees. Consider a rooted labelled tree in which each internal node has exactly [Formula: see text] children, [Formula: see text]. We first generalize the enumeration of labelled histories for a bifurcating tree ([Formula: see text]) to enumerate labelled histories for an [Formula: see text]-furcating tree with arbitrary [Formula: see text]. We formulate a conjecture for the rooted unlabelled [Formula: see text]-furcating tree shape on [Formula: see text] internal nodes whose labelled topologies have the most labelled histories. Finally, we enumerate labelled histories for [Formula: see text]-furcating trees in a setting that allows for simultaneous branchings. These results advance mathematical phylogenetic modelling by extending computations concerning fundamental features of bifurcating phylogenetic trees to a more general class of multifurcating trees.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Labelled histories with multifurcation and simultaneity.","authors":"Emily H Dickey, Noah A Rosenberg","doi":"10.1098/rstb.2023.0307","DOIUrl":"10.1098/rstb.2023.0307","url":null,"abstract":"<p><p>In mathematical models of phylogenetic trees evolving in time, a labelled history for a rooted labelled bifurcating tree is a temporal sequence of the branchings that give rise to the tree. That is, given a leaf-labelled tree with [Formula: see text] leaves and [Formula: see text] internal nodes, a labelled history is an identification between the internal nodes and the set [Formula: see text], such that the label assigned to a given node is strictly greater than the labels assigned to its descendants. We generalize the concept of labelled histories to [Formula: see text]-furcating trees. Consider a rooted labelled tree in which each internal node has exactly [Formula: see text] children, [Formula: see text]. We first generalize the enumeration of labelled histories for a bifurcating tree ([Formula: see text]) to enumerate labelled histories for an [Formula: see text]-furcating tree with arbitrary [Formula: see text]. We formulate a conjecture for the rooted unlabelled [Formula: see text]-furcating tree shape on [Formula: see text] internal nodes whose labelled topologies have the most labelled histories. Finally, we enumerate labelled histories for [Formula: see text]-furcating trees in a setting that allows for simultaneous branchings. These results advance mathematical phylogenetic modelling by extending computations concerning fundamental features of bifurcating phylogenetic trees to a more general class of multifurcating trees.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230307"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841368/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2024.0226
Cedric Chauve, Caroline Colijn, Louxin Zhang
Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation for rooted phylogenetic trees that encodes a tree on [Formula: see text] ordered taxa as a vector of length [Formula: see text] in which each taxon appears exactly twice. Using this new tree representation, we introduce a novel tree rearrangement operator, termed an HOP, that results in a tree space of linear diameter and quadratic neighbourhood size. We also introduce a novel metric, the HOP distance, which is the minimum number of HOPs to transform a tree into another tree. The HOP distance can be computed in near-linear time-a rare instance of tree rearrangement distance that is tractable. Our experiments show that the HOP distance is better correlated to the Subtree-Prune-and-Regraft distance than the widely used Robinson-Foulds distance. We also describe how the proposed tree representation can be further generalized to tree-child networks, showcasing its versatility and potential applications in broader evolutionary analyses.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"A vector representation for phylogenetic trees.","authors":"Cedric Chauve, Caroline Colijn, Louxin Zhang","doi":"10.1098/rstb.2024.0226","DOIUrl":"10.1098/rstb.2024.0226","url":null,"abstract":"<p><p>Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation for rooted phylogenetic trees that encodes a tree on [Formula: see text] ordered taxa as a vector of length [Formula: see text] in which each taxon appears exactly twice. Using this new tree representation, we introduce a novel tree rearrangement operator, termed an <i>HOP</i>, that results in a tree space of linear diameter and quadratic neighbourhood size. We also introduce a novel metric, the <i>HOP distance</i>, which is the minimum number of HOPs to transform a tree into another tree. The HOP distance can be computed in near-linear time-a rare instance of tree rearrangement distance that is tractable. Our experiments show that the HOP distance is better correlated to the Subtree-Prune-and-Regraft distance than the widely used Robinson-Foulds distance. We also describe how the proposed tree representation can be further generalized to tree-child networks, showcasing its versatility and potential applications in broader evolutionary analyses.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20240226"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0305
Amaury Lambert
The paper written in 1925 by G. Udny Yule that we celebrate in this special issue introduces several novelties and results that we recall in detail. First, we discuss Yule's (1925)main legacies over the past century, focusing on empirical frequency distributions with heavy tails and random tree models for phylogenies. We estimate the year when Yule's work was re-discovered by scientists interested in stochastic processes of population growth (1948) and the year from which it began to be cited (1951, Yule's death). We highlight overlooked aspects of Yule's work (e.g. the Yule process of Yule processes) and correct some common misattributions (e.g. the Yule tree). Second, we generalize Yule's results on the average frequency of genera of a given age and size (number of species). We show that his formula also applies to the age [Formula: see text] and size [Formula: see text] of any randomly chosen genus and that the pairs [Formula: see text] are equally distributed and independent across genera. This property extends to triples [Formula: see text], where [Formula: see text] are the coalescence times of the genus phylogeny, even when species diversification within genera follows any integer-valued process, including species extinctions. Studying [Formula: see text] in this broader context allows us to identify cases where [Formula: see text] has a power-law tail distribution, with new applications to urn schemes.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Ages, sizes and (trees within) trees of taxa and of urns, from Yule to today.","authors":"Amaury Lambert","doi":"10.1098/rstb.2023.0305","DOIUrl":"10.1098/rstb.2023.0305","url":null,"abstract":"<p><p>The paper written in 1925 by G. Udny Yule that we celebrate in this special issue introduces several novelties and results that we recall in detail. First, we discuss Yule's (1925)main legacies over the past century, focusing on empirical frequency distributions with heavy tails and random tree models for phylogenies. We estimate the year when Yule's work was re-discovered by scientists interested in stochastic processes of population growth (1948) and the year from which it began to be cited (1951, Yule's death). We highlight overlooked aspects of Yule's work (e.g. the Yule process of Yule processes) and correct some common misattributions (e.g. the Yule tree). Second, we generalize Yule's results on the average frequency of genera of a given age and size (number of species). We show that his formula also applies to the age [Formula: see text] and size [Formula: see text] of any randomly chosen genus and that the pairs [Formula: see text] are equally distributed and independent across genera. This property extends to triples [Formula: see text], where [Formula: see text] are the coalescence times of the genus phylogeny, even when species diversification within genera follows any integer-valued process, including species extinctions. Studying [Formula: see text] in this broader context allows us to identify cases where [Formula: see text] has a power-law tail distribution, with new applications to urn schemes.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230305"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0310
Benjamin Teo, Paul Bastide, Cécile Ané
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture. Computing the likelihood of data observed at the leaves is costly as the size and complexity of the phylogeny grows. Efficient algorithms exist for trees, but cannot be applied to networks. We show that a vast array of models for trait evolution along phylogenetic networks can be reformulated as graphical models, for which efficient belief propagation algorithms exist. We provide a brief review of belief propagation on general graphical models, then focus on linear Gaussian models for continuous traits. We show how belief propagation techniques can be applied for exact or approximate (but more scalable) likelihood and gradient calculations, and prove novel results for efficient parameter inference of some models. We highlight the possible fruitful interactions between graphical models and phylogenetic methods. For example, approximate likelihood approaches have the potential to greatly reduce computational costs for phylogenies with reticulations.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Leveraging graphical model techniques to study evolution on phylogenetic networks.","authors":"Benjamin Teo, Paul Bastide, Cécile Ané","doi":"10.1098/rstb.2023.0310","DOIUrl":"10.1098/rstb.2023.0310","url":null,"abstract":"<p><p>The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture. Computing the likelihood of data observed at the leaves is costly as the size and complexity of the phylogeny grows. Efficient algorithms exist for trees, but cannot be applied to networks. We show that a vast array of models for trait evolution along phylogenetic networks can be reformulated as graphical models, for which efficient belief propagation algorithms exist. We provide a brief review of belief propagation on general graphical models, then focus on linear Gaussian models for continuous traits. We show how belief propagation techniques can be applied for exact or approximate (but more scalable) likelihood and gradient calculations, and prove novel results for efficient parameter inference of some models. We highlight the possible fruitful interactions between graphical models and phylogenetic methods. For example, approximate likelihood approaches have the potential to greatly reduce computational costs for phylogenies with reticulations.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230310"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0308
Mike Steel
A wide variety of stochastic models of cladogenesis (based on speciation and extinction) lead to an identical distribution on phylogenetic tree shapes once the edge lengths are ignored. By contrast, the distribution of the tree's edge lengths is generally quite sensitive to the underlying model. In this paper, we review the impact of different model choices on tree shape and edge length distribution, and its impact for studying the properties of phylogenetic diversity (PD) as a measure of biodiversity, and the loss of PD as species become extinct at the present. We also compare PD with a stochastic model of feature diversity, and investigate some mathematical links and inequalities between these two measures plus their predictions concerning the loss of biodiversity under extinction at the present.This article is part of the theme issue "'A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Neutral phylogenetic models and their role in tree-based biodiversity measures.","authors":"Mike Steel","doi":"10.1098/rstb.2023.0308","DOIUrl":"10.1098/rstb.2023.0308","url":null,"abstract":"<p><p>A wide variety of stochastic models of cladogenesis (based on speciation and extinction) lead to an identical distribution on phylogenetic tree shapes once the edge lengths are ignored. By contrast, the distribution of the tree's edge lengths is generally quite sensitive to the underlying model. In this paper, we review the impact of different model choices on tree shape and edge length distribution, and its impact for studying the properties of phylogenetic diversity (PD) as a measure of biodiversity, and the loss of PD as species become extinct at the present. We also compare PD with a stochastic model of feature diversity, and investigate some mathematical links and inequalities between these two measures plus their predictions concerning the loss of biodiversity under extinction at the present.This article is part of the theme issue \"'A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230308"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0304
Michael Fuchs
Shape parameters, e.g. balance indices, of evolutionary trees have been extensively studied under the Yule model in phylogenetics. Independently, many of the same parameters have also been studied for random binary search trees in computer science, where they measure the running time of algorithms. In fact, under the Yule and binary search tree models, these parameters have the same distribution, resulting in many identical discoveries. In this survey, we explain these connections and introduce some of the tools that have been used in computer science to derive stochastic results for shape parameters.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Shape parameters of evolutionary trees in theoretical computer science.","authors":"Michael Fuchs","doi":"10.1098/rstb.2023.0304","DOIUrl":"10.1098/rstb.2023.0304","url":null,"abstract":"<p><p>Shape parameters, e.g. balance indices, of evolutionary trees have been extensively studied under the Yule model in phylogenetics. Independently, many of the same parameters have also been studied for random binary search trees in computer science, where they measure the running time of algorithms. In fact, under the Yule and binary search tree models, these parameters have the same distribution, resulting in many identical discoveries. In this survey, we explain these connections and introduce some of the tools that have been used in computer science to derive stochastic results for shape parameters.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230304"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0301
François Bienvenu
Models of random phylogenetic networks have been used since the inception of the field, but the introduction and rigorous study of mathematically tractable models is a much more recent topic that has gained momentum in the last 5 years. This manuscript discusses some recent developments in the field through a selection of examples. The emphasis is on the techniques rather than on the results themselves, and on probabilistic tools rather than on combinatorial ones.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Mathematically tractable models of random phylogenetic networks: an overview of some recent developments.","authors":"François Bienvenu","doi":"10.1098/rstb.2023.0301","DOIUrl":"10.1098/rstb.2023.0301","url":null,"abstract":"<p><p>Models of random phylogenetic networks have been used since the inception of the field, but the introduction and rigorous study of mathematically tractable models is a much more recent topic that has gained momentum in the last 5 years. This manuscript discusses some recent developments in the field through a selection of examples. The emphasis is on the techniques rather than on the results themselves, and on probabilistic tools rather than on combinatorial ones.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230301"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13Epub Date: 2025-02-20DOI: 10.1098/rstb.2023.0315
Will Dumm, Duncan Ralph, William DeWitt, Ashni Vora, Tatsuya Araki, Gabriel D Victora, Frederick A Matsen Iv
The phylogenetic inference package GCtree uses abundance of sampled sequences to improve the performance of parsimony-based inference, using a branching process model. Our previous work showed that GCtree performs competitively on B-cell receptor data, compared with other similar tools. In this article, we describe recent enhancements to GCtree, including an efficient tree storage data structure that discovers additional diversity of parsimonious trees with negligible additional computational cost. We also describe a suite of new objective functions that can be used to rank these trees, including a Poisson context likelihood function that models sequence evolution in a context-sensitive way. We validate these additions to GCtree with simulated B-cell receptor data, and benchmark performance against other phylogenetic inference tools.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
{"title":"Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.","authors":"Will Dumm, Duncan Ralph, William DeWitt, Ashni Vora, Tatsuya Araki, Gabriel D Victora, Frederick A Matsen Iv","doi":"10.1098/rstb.2023.0315","DOIUrl":"10.1098/rstb.2023.0315","url":null,"abstract":"<p><p>The phylogenetic inference package GCtree uses abundance of sampled sequences to improve the performance of parsimony-based inference, using a branching process model. Our previous work showed that GCtree performs competitively on B-cell receptor data, compared with other similar tools. In this article, we describe recent enhancements to GCtree, including an efficient tree storage data structure that discovers additional diversity of parsimonious trees with negligible additional computational cost. We also describe a suite of new objective functions that can be used to rank these trees, including a Poisson context likelihood function that models sequence evolution in a context-sensitive way. We validate these additions to GCtree with simulated B-cell receptor data, and benchmark performance against other phylogenetic inference tools.This article is part of the theme issue '\"A mathematical theory of evolution\": phylogenetic models dating back 100 years'.</p>","PeriodicalId":19872,"journal":{"name":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"380 1919","pages":"20230315"},"PeriodicalIF":5.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867150/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}