Systematic Biology最新文献

筛选
英文 中文
Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards. 化石记录中能发现现代隐性物种吗?姬蛙蜥个案研究。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-11-22 DOI: 10.1093/sysbio/syae067
Till Ramm, Jaimi A Gray, Christy A Hipsley, Scott Hocknull, Jane Melville, Johannes Müller
{"title":"Are Modern Cryptic Species Detectable in the Fossil Record? A Case Study on Agamid Lizards.","authors":"Till Ramm, Jaimi A Gray, Christy A Hipsley, Scott Hocknull, Jane Melville, Johannes Müller","doi":"10.1093/sysbio/syae067","DOIUrl":"https://doi.org/10.1093/sysbio/syae067","url":null,"abstract":"<p><p>Comparisons of extant and extinct biodiversity are often dependent on objective morphology-based identifications of fossils and assume a well-established and comparable taxonomy for both fossil and modern taxa. However, since many modern (cryptic) species are delimitated mainly via external morphology and / or molecular data, it is often unclear to what degree fossilized (osteological) remains allow classification to a similar level. When intraspecific morphological variation in extant taxa is poorly known, the definition of extinct species as well as the referral of fossils to extant species can be heavily biased, particularly if fossils are represented by incomplete isolated skeletal elements. This problem is especially pronounced in squamates (lizards and snakes) owing to a lack of osteological comparative knowledge for many lower taxonomic groups, concomitant with a recent increase of molecular studies revealing great cryptic diversity. Here, we apply a quantitative approach using 3D geometric morphometrics on 238 individuals of 14 genera of extant Australian and Papua New Guinean agamid lizards to test the value of two isolated skull bones (frontals and maxillae) for inferring taxonomic and ecological affinities. We further test for the consistency of intra- and interspecific morphological variability of these elements as a proxy for extinct taxonomic richness. We show that both bones are diagnostic at the generic level, and both can infer microhabitat and are of palaeoecological utility. However, species-level diversity is likely underestimated by both elements, with ~30-40% of species pairs showing no significant differences in shape. Mean intraspecific morphological variability is largely consistent across species and bones and thus a useful proxy for extinct species diversity. Reducing sample size and landmark completeness to approximate fossil specimens led to decreased classification accuracy and increased variance of morphological disparity, raising further doubts on the transferability of modern species borders to the fossil record of agamids. Our results highlight the need to establish appropriate levels of morphology-based taxonomic or ecological groupings prior to comparing extant and extinct biodiversity.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688897","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
Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal 测试多种区域特征与物种形成、灭绝和扩散的生物地理过程之间的关系
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2024-11-20 DOI: 10.1093/sysbio/syae062
Sarah K Swiston, Michael J Landis
{"title":"Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal","authors":"Sarah K Swiston, Michael J Landis","doi":"10.1093/sysbio/syae062","DOIUrl":"https://doi.org/10.1093/sysbio/syae062","url":null,"abstract":"The spatial and environmental features of regions where clades are evolving are expected to impact biogeographic processes such as speciation, extinction, and dispersal. Any number of regional features (such as elevation, distance, area, etc.) may be directly or indirectly related to these processes. For example, it may be that distances or differences in elevation or both may limit dispersal rates. However, it is difficult to disentangle which features are most strongly related to rates of different processes. Here, we present an extensible Multi-feature Feature-Informed GeoSSE (MultiFIG) model that allows for the simultaneous investigation of any number of regional features. MultiFIG provides a conceptual framework for incorporating large numbers of features of different types, including categorical, quantitative, within-region, and between-region features, along with a mathematical framework for translating those features into biogeographic rates for statistical hypothesis testing. Using traditional Bayesian parameter estimation and reversible-jump Markov chain Monte Carlo, MultiFIG allows for the exploration of models with different numbers and combinations of feature-effect parameters, and generates estimates for the strengths of relationships between each regional feature and core process. We validate this model with a simulation study covering a range of scenarios with different numbers of regions, tree sizes, and feature values. We also demonstrate the application of MultiFIG with an empirical case study of the South American lizard genus Liolaemus, investigating sixteen regional features related to area, distance, and elevation. Our results show two important feature-process relationships: a negative distance/dispersal relationship, and a negative area/extinction relationship. Interestingly, although speciation rates were found to be higher in Andean versus non-Andean regions, the model did not assign significance to Andean- or elevation-related parameters. These results highlight the need to consider multiple regional features in biogeographic hypothesis testing.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"191 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142678579","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
Robustness of Divergence Time Estimation Despite Gene Tree Estimation Error: A Case Study of Fireflies (Coleoptera: Lampyridae) 尽管存在基因树估计误差,但分化时间估计的稳健性:萤火虫(鞘翅目:灯蛾科)案例研究
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2024-11-13 DOI: 10.1093/sysbio/syae065
Sebastian Höhna, Sarah E Lower, Pablo Duchen, Ana Catalán
{"title":"Robustness of Divergence Time Estimation Despite Gene Tree Estimation Error: A Case Study of Fireflies (Coleoptera: Lampyridae)","authors":"Sebastian Höhna, Sarah E Lower, Pablo Duchen, Ana Catalán","doi":"10.1093/sysbio/syae065","DOIUrl":"https://doi.org/10.1093/sysbio/syae065","url":null,"abstract":"Genomic data has become ubiquitous in phylogenomic studies, including divergence time estimation, but provide new challenges. These challenges include, amongst others, biological gene tree discordance, methodological gene tree estimation error, and computational limitations on performing full Bayesian inference under complex models. In this study, we use a recently published firefly (Coleoptera: Lampyridae) anchored hybrid enrichment dataset (AHE; 436 loci for 88 Lampyridae species and 10 outgroup species) as a case study to explore gene tree estimation error and the robustness of divergence time estimation. First, we explored the amount of model violation using posterior predictive simulations because model violations are likely to bias phylogenetic inferences and produce gene tree estimation error. We specifically focused on missing data (either uniformly distributed or systematically) and the distribution of highly variable and conserved sites (either uniformly distributed or clustered). Our assessment of model adequacy showed that standard phylogenetic substitution models are not adequate for any of the 436 AHE loci. We tested if the model violations and alignment errors resulted indeed in gene tree estimation error by comparing the observed gene tree discordance to simulated gene tree discordance under the multispecies coalescent model. Thus, we show that the inferred gene tree discordance is not only due to biological mechanism but primarily due to inference errors. Lastly, we explored if divergence time estimation is robust despite the observed gene tree estimation error. We selected four subsets of the full AHE dataset, concatenated each subset and performed a Bayesian relaxed clock divergence estimation in RevBayes. The estimated divergence times overlapped for all nodes that are shared between the topologies. Thus, divergence time estimation is robust using any well selected data subset as long as the topology inference is robust.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"20 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610475","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
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama. 拓扑测试和人口模型揭示了巴拿马地峡形成后大加勒比海的新物种演化途径。
IF 6.1 1区 生物学
Systematic Biology Pub Date : 2024-10-30 DOI: 10.1093/sysbio/syae045
Benjamin M Titus, H Lisle Gibbs, Nuno Simões, Marymegan Daly
{"title":"Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.","authors":"Benjamin M Titus, H Lisle Gibbs, Nuno Simões, Marymegan Daly","doi":"10.1093/sysbio/syae045","DOIUrl":"10.1093/sysbio/syae045","url":null,"abstract":"<p><p>Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"758-768"},"PeriodicalIF":6.1,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141749074","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
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
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