Systematic Biology最新文献

筛选
英文 中文
The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics. 贝叶斯形态系统学中特征编码的基本作用。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae033
Basanta Khakurel, Courtney Grigsby, Tyler D Tran, Juned Zariwala, Sebastian Höhna, April M Wright
{"title":"The Fundamental Role of Character Coding in Bayesian Morphological Phylogenetics.","authors":"Basanta Khakurel, Courtney Grigsby, Tyler D Tran, Juned Zariwala, Sebastian Höhna, April M Wright","doi":"10.1093/sysbio/syae033","DOIUrl":"10.1093/sysbio/syae033","url":null,"abstract":"<p><p>Phylogenetic trees establish a historical context for the study of organismal form and function. Most phylogenetic trees are estimated using a model of evolution. For molecular data, modeling evolution is often based on biochemical observations about changes between character states. For example, there are 4 nucleotides, and we can make assumptions about the probability of transitions between them. By contrast, for morphological characters, we may not know a priori how many characters states there are per character, as both extant sampling and the fossil record may be highly incomplete, which leads to an observer bias. For a given character, the state space may be larger than what has been observed in the sample of taxa collected by the researcher. In this case, how many evolutionary rates are needed to even describe transitions between morphological character states may not be clear, potentially leading to model misspecification. To explore the impact of this model misspecification, we simulated character data with varying numbers of character states per character. We then used the data to estimate phylogenetic trees using models of evolution with the correct number of character states and an incorrect number of character states. The results of this study indicate that this observer bias may lead to phylogenetic error, particularly in the branch lengths of trees. If the state space is wrongly assumed to be too large, then we underestimate the branch lengths, and the opposite occurs when the state space is wrongly assumed to be too small.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"861-871"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141535331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies. 全基因组揭示 Neodiprion 锯蝇基因树不一致的进化关系和机制
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae036
Danielle K Herrig, Ryan D Ridenbaugh, Kim L Vertacnik, Kathryn M Everson, Sheina B Sim, Scott M Geib, David W Weisrock, Catherine R Linnen
{"title":"Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies.","authors":"Danielle K Herrig, Ryan D Ridenbaugh, Kim L Vertacnik, Kathryn M Everson, Sheina B Sim, Scott M Geib, David W Weisrock, Catherine R Linnen","doi":"10.1093/sysbio/syae036","DOIUrl":"10.1093/sysbio/syae036","url":null,"abstract":"<p><p>Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting (ILS) and introgression. Here, we use a whole-genome alignment, multiple locus-sampling strategies, and summary-tree and single nucleotide polymorphism-based species-tree methods to infer a species tree for eastern North American Neodiprion species, a clade of pine-feeding sawflies (Order: Hymenopteran; Family: Diprionidae). We recovered a well-supported species tree that-except for three uncertain relationships-was robust to different strategies for analyzing whole-genome data. Nevertheless, underlying gene-tree discordance was high. To understand this genealogical variation, we used multiple linear regression to model site concordance factors estimated in 50-kb windows as a function of several genomic predictor variables. We found that site concordance factors tended to be higher in regions of the genome with more parsimony-informative sites, fewer singletons, less missing data, lower GC content, more genes, lower recombination rates, and lower D-statistics (less introgression). Together, these results suggest that ILS, introgression, and genotyping error all shape the genomic landscape of gene-tree discordance in Neodiprion. More generally, our findings demonstrate how combining phylogenomic analysis with knowledge of local genomic features can reveal mechanisms that produce topological heterogeneity across genomes.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"839-860"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation. 系统发育估计的半监督学习方法。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae029
Daniele Silvestro, Thibault Latrille, Nicolas Salamin
{"title":"Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation.","authors":"Daniele Silvestro, Thibault Latrille, Nicolas Salamin","doi":"10.1093/sysbio/syae029","DOIUrl":"10.1093/sysbio/syae029","url":null,"abstract":"<p><p>Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our understanding of the underlying biological processes, such as nucleotide substitutions, and the estimation of model parameters by maximum likelihood or Bayesian inference. However, deriving and optimizing the likelihood of the data is not always possible under complex evolutionary scenarios or even tractable for large datasets, often leading to unrealistic simplifying assumptions in the fitted models. To overcome this issue, we coupled stochastic simulations of genome evolution with a new supervised deep-learning model to infer key parameters of molecular evolution. Our model is designed to directly analyze multiple sequence alignments and estimate per-site evolutionary rates and divergence without requiring a known phylogenetic tree. The accuracy of our predictions matched that of likelihood-based phylogenetic inference when rate heterogeneity followed a simple gamma distribution, but it strongly exceeded it under more complex patterns of rate variation, such as codon models. Our approach is highly scalable and can be efficiently applied to genomic data, as we showed on a dataset of 26 million nucleotides from the clownfish clade. Our simulations also showed that the integration of per-site rates obtained by deep learning within a Bayesian framework led to significantly more accurate phylogenetic inference, particularly with respect to the estimated branch lengths. We thus propose that future advancements in phylogenetic analysis will benefit from a semi-supervised learning approach that combines deep-learning estimation of substitution rates, which allows for more flexible models of rate variation, and probabilistic inference of the phylogenetic tree, which guarantees interpretability and a rigorous assessment of statistical support.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"789-806"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11639169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model. 期望最大化使分类率模型下的系统发育约会成为可能
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae034
Uyen Mai, Eduardo Charvel, Siavash Mirarab
{"title":"Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.","authors":"Uyen Mai, Eduardo Charvel, Siavash Mirarab","doi":"10.1093/sysbio/syae034","DOIUrl":"10.1093/sysbio/syae034","url":null,"abstract":"<p><p>Dating phylogenetic trees to obtain branch lengths in time units is essential for many downstream applications but has remained challenging. Dating requires inferring substitution rates that can change across the tree. While we can assume to have information about a small subset of nodes from the fossil record or sampling times (for fast-evolving organisms), inferring the ages of the other nodes essentially requires extrapolation and interpolation. Assuming a distribution of branch rates, we can formulate dating as a constrained maximum likelihood (ML) estimation problem. While ML dating methods exist, their accuracy degrades in the face of model misspecification, where the assumed parametric statistical distribution of branch rates vastly differs from the true distribution. Notably, most existing methods assume rigid, often unimodal, branch rate distributions. A second challenge is that the likelihood function involves an integral over the continuous domain of the rates, often leading to difficult non-convex optimization problems. To tackle both challenges, we propose a new method called Molecular Dating using Categorical-models (MD-Cat). MD-Cat uses a categorical model of rates inspired by non-parametric statistics and can approximate a large family of models by discretizing the rate distribution into k categories. Under this model, we can use the Expectation-Maximization algorithm to co-estimate rate categories and branch lengths in time units. Our model has fewer assumptions about the true distribution of branch rates than parametric models such as Gamma or LogNormal distribution. Our results on two simulated and real datasets of Angiosperms and HIV and a wide selection of rate distributions show that MD-Cat is often more accurate than the alternatives, especially on datasets with exponential or multimodal rate distributions.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"823-838"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation. 在存在物种间速率变异的情况下,实现可靠的引种检测。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae028
Thore Koppetsch, Milan Malinsky, Michael Matschiner
{"title":"Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.","authors":"Thore Koppetsch, Milan Malinsky, Michael Matschiner","doi":"10.1093/sysbio/syae028","DOIUrl":"10.1093/sysbio/syae028","url":null,"abstract":"<p><p>The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report \"ancient introgression\"- referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"769-788"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11639170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Adaptive Radiation Without Independent Stages of Trait Evolution in a Group of Caribbean Anoles. 加勒比鼹鼠群中没有独立性状进化阶段的适应性辐射。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae041
Brooke Bodensteiner, Edward D Burress, Martha M Muñoz
{"title":"Adaptive Radiation Without Independent Stages of Trait Evolution in a Group of Caribbean Anoles.","authors":"Brooke Bodensteiner, Edward D Burress, Martha M Muñoz","doi":"10.1093/sysbio/syae041","DOIUrl":"10.1093/sysbio/syae041","url":null,"abstract":"<p><p>Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a \"stages\" model, with some traits saturating early in a lineage's history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, corresponding to independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"743-757"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Caught in the Act: Incipient Speciation at the Southern Limit of Viburnum in the Central Andes. 被逮个正着:安第斯山脉中部紫云英南缘的物种萌芽。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-25 DOI: 10.1093/sysbio/syae023
Carlos A Maya-Lastra, Patrick W Sweeney, Deren A R Eaton, Vania Torrez, Carla Maldonado, Malu I Ore-Rengifo, Mónica Arakaki, Michael J Donoghue, Erika J Edwards
{"title":"Caught in the Act: Incipient Speciation at the Southern Limit of Viburnum in the Central Andes.","authors":"Carlos A Maya-Lastra, Patrick W Sweeney, Deren A R Eaton, Vania Torrez, Carla Maldonado, Malu I Ore-Rengifo, Mónica Arakaki, Michael J Donoghue, Erika J Edwards","doi":"10.1093/sysbio/syae023","DOIUrl":"10.1093/sysbio/syae023","url":null,"abstract":"<p><p>A fundamental objective of evolutionary biology is to understand the origin of independently evolving species. Phylogenetic studies of species radiations rarely are able to document ongoing speciation; instead, modes of speciation, entailing geographic separation and/or ecological differentiation, are posited retrospectively. The Oreinotinus clade of Viburnum has radiated recently from north to south through the cloud forests of Mexico and Central America to the Central Andes. Our analyses support a hypothesis of incipient speciation in Oreinotinus at the southern edge of its geographic range, from central Peru to northern Argentina. Although several species and infraspecific taxa have been recognized in this area, multiple lines of evidence and analytical approaches (including analyses of phylogenetic relationships, genetic structure, leaf morphology, and climatic envelopes) favor the recognition of just a single species, V. seemenii. We show that what has previously been recognized as V. seemenii f. minor has recently occupied the drier Tucuman-Bolivian forest region from Samaipata in Bolivia to Salta in northern Argentina. Plants in these populations form a well-supported clade with a distinctive genetic signature and they have evolved smaller, narrower leaves. We interpret this as the beginning of a within-species divergence process that has elsewhere in the neotropics resulted repeatedly in Viburnum species with a particular set of leaf ecomorphs. Specifically, the southern populations are in the process of evolving the small, glabrous, and entire leaf ecomorph that has evolved in four other montane areas of endemism. As predicted based on our studies of leaf ecomorphs in Chiapas, Mexico, these southern populations experience generally drier conditions, with large diurnal temperature fluctuations. In a central portion of the range of V. seemenii, characterized by wetter climatic conditions, we also document what may be the initial differentiation of the leaf ecomorph with larger, pubescent, and toothy leaves. The emergence of these ecomorphs thus appears to be driven by adaptation to subtly different climatic conditions in separate geographic regions, as opposed to parapatric differentiation along elevational gradients as suggested by Viburnum species distributions in other parts of the neotropics.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"629-643"},"PeriodicalIF":6.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141238062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria. 随机特征映射、贝叶斯模型选择和生物合成途径为蓝藻栖息地偏好的进化提供了新线索
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-25 DOI: 10.1093/sysbio/syae025
Giorgio Bianchini, Martin Hagemann, Patricia Sánchez-Baracaldo
{"title":"Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria.","authors":"Giorgio Bianchini, Martin Hagemann, Patricia Sánchez-Baracaldo","doi":"10.1093/sysbio/syae025","DOIUrl":"10.1093/sysbio/syae025","url":null,"abstract":"<p><p>Cyanobacteria are the only prokaryotes to have evolved oxygenic photosynthesis paving the way for complex life. Studying the evolution and ecological niche of cyanobacteria and their ancestors is crucial for understanding the intricate dynamics of biosphere evolution. These organisms frequently deal with environmental stressors such as salinity and drought, and they employ compatible solutes as a mechanism to cope with these challenges. Compatible solutes are small molecules that help maintain cellular osmotic balance in high-salinity environments, such as marine waters. Their production plays a crucial role in salt tolerance, which, in turn, influences habitat preference. Among the 5 known compatible solutes produced by cyanobacteria (sucrose, trehalose, glucosylglycerol, glucosylglycerate, and glycine betaine), their synthesis varies between individual strains. In this study, we work in a Bayesian stochastic mapping framework, integrating multiple sources of information about compatible solute biosynthesis in order to predict the ancestral habitat preference of Cyanobacteria. Through extensive model selection analyses and statistical tests for correlation, we identify glucosylglycerol and glucosylglycerate as the most significantly correlated with habitat preference, while trehalose exhibits the weakest correlation. Additionally, glucosylglycerol, glucosylglycerate, and glycine betaine show high loss/gain rate ratios, indicating their potential role in adaptability, while sucrose and trehalose are less likely to be lost due to their additional cellular functions. Contrary to previous findings, our analyses predict that the last common ancestor of Cyanobacteria (living at around 3180 Ma) had a 97% probability of a high salinity habitat preference and was likely able to synthesize glucosylglycerol and glucosylglycerate. Nevertheless, cyanobacteria likely colonized low-salinity environments shortly after their origin, with an 89% probability of the first cyanobacterium with low-salinity habitat preference arising prior to the Great Oxygenation Event (2460 Ma). Stochastic mapping analyses provide evidence of cyanobacteria inhabiting early marine habitats, aiding in the interpretation of the geological record. Our age estimate of ~2590 Ma for the divergence of 2 major cyanobacterial clades (Macro- and Microcyanobacteria) suggests that these were likely significant contributors to primary productivity in marine habitats in the lead-up to the Great Oxygenation Event, and thus played a pivotal role in triggering the sudden increase in atmospheric oxygen.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"644-665"},"PeriodicalIF":6.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11505929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141459410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference 分类群添加后系统发生树的不稳定性:经验频率、可预测性和在线推断的后果
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2024-10-25 DOI: 10.1093/sysbio/syae059
Lena Collienne, Mary Barker, Marc A Suchard, Frederick A Matsen IV
{"title":"Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference","authors":"Lena Collienne, Mary Barker, Marc A Suchard, Frederick A Matsen IV","doi":"10.1093/sysbio/syae059","DOIUrl":"https://doi.org/10.1093/sysbio/syae059","url":null,"abstract":"Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred tree. In this paper, we analyze the stability of single taxon addition in a Maximum Likelihood framework across 1, 000 empirical datasets. We find that instability occurs in almost 90% of our examples, although observed topological differences do not always reach significance under the AU-test. Changes in tree topology after addition of a taxon rarely occur close to its attachment location, and are more frequently observed in more distant tree locations carrying low bootstrap support. To investigate whether instability is predictable, we hypothesize sources of instability and design summary statistics addressing these hypotheses. Using these summary statistics as input features for machine learning under random forests, we are able to predict instability and can identify the most influential features. In summary, it does not appear that a strict insertion-only online inference method will deliver globally optimal trees, although relaxing insertion strictness by allowing for a small number of final tree rearrangements or accepting slightly suboptimal solutions appears feasible.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"31 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142490398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data 从转录组数据中推断出Acoelomorpha的系统进化骨架
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2024-10-25 DOI: 10.1093/sysbio/syae057
Samuel Abalde, Ulf Jondelius
{"title":"A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data","authors":"Samuel Abalde, Ulf Jondelius","doi":"10.1093/sysbio/syae057","DOIUrl":"https://doi.org/10.1093/sysbio/syae057","url":null,"abstract":"Xenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs –which include three main groups: Acoela, Nemertodermatida, and Xenoturbella– have been proposed to be an early diverging Bilateria, sister to protostomes and deuterostomes, but other phylogenomic analyses have recovered this clade nested within the deuterostomes, as sister to Ambulacraria. The position of Xenacoelomorpha within the metazoan tree has understandably attracted a lot of attention, overshadowing the study of phylogenetic relationships within this group. Given that Xenoturbella includes only six species whose relationships are well understood, we decided to focus on the most speciose Acoelomorpha (Acoela + Nemertodermatida). Here, we have sequenced 29 transcriptomes, doubling the number of sequenced species, to infer a backbone tree for Acoelomorpha based on genomic data. The recovered topology is mostly congruent with previous studies. The most important difference is the recovery of Paratomella as the first off-shoot within Acoela, dramatically changing the reconstruction of the ancestral acoel. Besides, we have detected incongruence between the gene trees and the species tree, likely linked to incomplete lineage sorting, and some signal of introgression between the families Dakuidae and Mecynostomidae, which hampers inferring the correct placement of this family and, particularly, of the genus Notocelis. We have also used this dataset to infer for the first time diversification times within Acoelomorpha, which coincide with known bilaterian diversification and extinction events. Given the importance of morphological data in acoelomorph phylogenetics, we tested several partitions and models. Although morphological data failed to recover a robust phylogeny, phylogenetic placement has proven to be a suitable alternative when a reference phylogeny is available.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"97 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信