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Cold Origins Limit the Establishment of Northern Temperate Plants in the Southern Hemisphere. 寒冷起源限制了北半球北温带植物的建立。
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2026-04-29 DOI: 10.1093/sysbio/syag036
William H Brightly,Siri Fjellheim,Thomas Lux,Mark D Mullinger,Colin P Osborne,Jill C Preston,Simen R Sandve,Maria S Vorontsova,Luke T Dunning
{"title":"Cold Origins Limit the Establishment of Northern Temperate Plants in the Southern Hemisphere.","authors":"William H Brightly,Siri Fjellheim,Thomas Lux,Mark D Mullinger,Colin P Osborne,Jill C Preston,Simen R Sandve,Maria S Vorontsova,Luke T Dunning","doi":"10.1093/sysbio/syag036","DOIUrl":"https://doi.org/10.1093/sysbio/syag036","url":null,"abstract":"Plants with amphitropical distributions have closely related populations in both Northern and Southern Hemispheres, but are absent from the intervening tropics. They provide a unique opportunity to study the constraints shaping the distribution of temperate lineages through time. Using grasses from the ecologically diverse supertribe Melicodae, an emerging study system with species distributed throughout the temperate regions, we test the hypothesis that geography and/or environmental niche constrain which lineages successfully cross the tropics to establish in the opposite hemisphere. Biogeographic and evolutionary modelling was conducted on well resolved plastid and nuclear phylogenies constructed from whole-genome sequencing of 178 accessions of 103 Melicodae species. Results show that species from cold regions are much less likely to successfully cross the tropics, with successful lineages all sharing warmer niches that evolved prior to their establishment in the opposite hemisphere. Evidence suggests that this result is explained both by the greater distances that high-latitude, cold-origin lineages must disperse to cross the tropics, and inherent limitations associated with colder thermal niches. In particular, our results suggest that traits allowing species to cope with cold winters, rather than an inability to cope with warm summers, limit their ability to establish in the opposite hemisphere, hinting at important trade-offs between cold-tolerance and biogeographic potential. These results provide insight into the drivers of the distribution and diversity of plants, and the challenges facing cold-origin lineages in a rapidly warming world. If cold-origin species occupy a smaller proportion of their potential range, and are unlikely to establish in new areas with suitable climates, their ability to track preferred habitat as climates warm may be worse than currently expected.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"154 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147754990","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
Phylogenomic discordances reveal conflicting hybridization episodes and widespread lineage-sorting events in temperate Loliinae grasses 系统基因组的不一致揭示了温带禾本科禾本科植物中相互冲突的杂交事件和广泛的谱系分选事件
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2026-04-18 DOI: 10.1093/sysbio/syag035
María Fernanda Moreno-Aguilar, Chunlin Chen, Juan Viruel, Diana Calderón, Itziar Arnelas, Aminael Sánchez-Rodríguez, Wenli Chen, Juan Camilo Ospina, Gloria Martínez-Sagarra, Juan Antonio Devesa, Alan Stewart, Pilar Catalán
{"title":"Phylogenomic discordances reveal conflicting hybridization episodes and widespread lineage-sorting events in temperate Loliinae grasses","authors":"María Fernanda Moreno-Aguilar, Chunlin Chen, Juan Viruel, Diana Calderón, Itziar Arnelas, Aminael Sánchez-Rodríguez, Wenli Chen, Juan Camilo Ospina, Gloria Martínez-Sagarra, Juan Antonio Devesa, Alan Stewart, Pilar Catalán","doi":"10.1093/sysbio/syag035","DOIUrl":"https://doi.org/10.1093/sysbio/syag035","url":null,"abstract":"The grass subtribe Loliinae has great ecological and economic importance, as it includes community-dominant species of mountain grasslands and the most extensively cultivated pasture, fodder and turf grasses (fescues, ryegrasses). Resolving the phylogeny of recently evolved Loliinae lineages has proven challenging due to frequent introgressions and polyploidizations that occurred throughout their history. Here we present the first target-capture phylogeny of Loliinae using 270 orthologous single-copy nuclear coding loci for a large sample of 132 representative taxa, covering all its 29 evolutionary lineages. Additionally, we assembled plastome sequences to complement the inferred hybrid speciation history of the Loliinae. Concatenated maximum likelihood and multispecies coalescent trees of ortho-homeolog single-copy genes showed well-supported relationships for major lineages, which were generally consistent across analyses and genomes, and with previous taxonomic and phylogenetic findings. However, they also revealed high levels of both nuclear and cyto-nuclear discordances estimated to be caused by hybridization and incomplete lineage sorting. We complemented this with a phylogenetic network analysis with representative samples from the main clades to infer reticulation events in the evolution of these grasses. Furthermore, we performed gene tree – species tree reconciliation methods using gene duplication and loss models and multi-labeled trees for polyploidy analysis to estimate the proportion of duplicated genes and the nature of polyploidy of the major Loliinae lineages. These analyses agreed that the Fine-Leaved (FL) Loliinae clade could have evolved from hybridization between more ancestral Broad-Leaved (BL) Loliinae lineages and that both groups underwent ancestral and recent hybridizations. The time-calibrated phylogeny of for the main Loliinae clades supports an early Miocene origin for Loliinae and Mid-Late Miocene splits for its main BL and FL lineages, while current species-rich groups radiated in the Late Miocene. Hybridization tests of nuclear data and topological incongruence assays between the nuclear single-copy genes and plastome-based trees using various approaches and different sampling subsets confirmed the rampant hybridization experienced by Loliinae at deep and shallow nodes. However, hybridization rates differed from lineage to lineage within the major clades and were not correlated with time or ploidy level, but rather depended on their different propensities to hybridize with species within and/or outside their own clade. Our analyses detected high hybridization rates in four broad-leaved (Subulatae-Hawaiian, Tropical-South African, Mexico-Central-South American (MCSA I-II) and Leucopoa p. p.) and five fine-leaved Loliinae lineages (American II, Aulaxyper, Afroalpine, American-Neozeylandic, Australia-Tasmania) containing rogue species that probably originated from trans-clade crosses and are more likely to hybridize g","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"14 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147726040","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
An Evolving View of Character Macroevolution. 性格宏观演化的演化观。
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2026-04-10 DOI: 10.1093/sysbio/syag034
Carrie M Tribble,Jesús Martínez Gómez,Carl J Rothfels,Michael R May
{"title":"An Evolving View of Character Macroevolution.","authors":"Carrie M Tribble,Jesús Martínez Gómez,Carl J Rothfels,Michael R May","doi":"10.1093/sysbio/syag034","DOIUrl":"https://doi.org/10.1093/sysbio/syag034","url":null,"abstract":"Phenotypes serve as the interface between organisms and their environments and are thus pivotal for comprehensive biological understanding. However, comparative analyses of species' phenotypes must account for the non-independence of characters imposed by the branching pattern of macroevolution. Methods to account for this phylogenetic non-independence have historically been conceived of as their own subfield: phylogenetic comparative methods (PCMs). In this conceptualization, a researcher takes a pre-existing phylogeny and uses it to correct for the non-independence of the character data that they wish to analyze. Here we argue that parallel developments in scientific philosophy, data availability, computational capacity, and model development have enabled a new paradigm of character evolution, where patterns of character evolution are seen as intrinsically related to the diversification process, and thus should be inferred jointly with the tree rather than reconstructed on an existing phylogeny in a two-step process. In the context of this paradigm shift, we review historical milestones in studies of character macroevolution and discuss major recent conceptual and methodological advances, with an emphasis on the opportunities and insights provided by the joint-inference perspective. We include primers on current topics in character evolution where joint inference is particularly effective, including: (1) state-dependent speciation and extinction models and the importance of cladogenetic change; (2) jointly modeling discrete and continuous characters; (3) accounting for hidden process variation in character evolution; (4) joint inference in divergence-time estimation; (5) joint inference of phylogeny and ancestral states, and; (6) joint inference of alignment and phylogeny. The article concludes with a reflection on the future trajectory of these methods, emphasizing the interconnectedness of character evolution with broader processes in biology.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"223 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663733","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
Nemo knows: clownfishes differentiate cryptic host species across fine and broad geographic scales and reveal a diverse species complex in the clownfish-hosting sea anemones 尼莫知道:小丑鱼在精细和广泛的地理尺度上区分隐藏的宿主物种,并揭示了小丑鱼宿主海葵中多样化的物种综合体
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2026-04-09 DOI: 10.1093/sysbio/syag033
Tommaso Chiodo, Aurélien De Jode, Andrea M Quattrini, Miranda K Gibson, Catheline Y M Froehlich, Danwei Huang, Takuma Fujii, Kensuke Yanagi, James D Reimer, Anna Scott, Estefanía Rodríguez, Benjamin M Titus
{"title":"Nemo knows: clownfishes differentiate cryptic host species across fine and broad geographic scales and reveal a diverse species complex in the clownfish-hosting sea anemones","authors":"Tommaso Chiodo, Aurélien De Jode, Andrea M Quattrini, Miranda K Gibson, Catheline Y M Froehlich, Danwei Huang, Takuma Fujii, Kensuke Yanagi, James D Reimer, Anna Scott, Estefanía Rodríguez, Benjamin M Titus","doi":"10.1093/sysbio/syag033","DOIUrl":"https://doi.org/10.1093/sysbio/syag033","url":null,"abstract":"The symbiosis between clownfishes (or anemonefishes) and their host sea anemones ranks among the most recognizable animal interactions on the planet. Found on coral reef habitats across the Indian and Pacific Oceans, 28 recognized species of clownfishes adaptively radiated from a common ancestor to live obligately with only 10 nominal species of host sea anemones. Are the host sea anemones truly less diverse than clownfishes? Did the symbiosis with clownfishes trigger a reciprocal co-evolutionary response to the mutualism? To address these questions, we combined fine- and broad-scale biogeographic sampling with multiple independent genomic datasets for the bubble-tip sea anemone, Entacmaea quadricolor—the most common clownfish host anemone throughout the Indo-West Pacific. Fine-scale sampling and restriction site associated DNA sequencing (RADseq) throughout the Japanese Archipelago revealed three highly divergent cryptic species: two of which co-occur throughout the Ryukyu Islands and can be differentiated by the clownfish species they host. Remarkably, broader biogeographic sampling and bait-capture sequencing reveals that this pattern is not simply the result of local ecological processes unique to Japan, but part of a deeper evolutionary signal where some species of E. quadricolor serve as host to the generalist clownfish species Amphiprion clarkii and others serve as host to the specialist clownfish A. frenatus. In total, we delimit six cryptic species in E. quadricolor that have diversified within the last five million years. The rapid speciation of E. quadricolor combined with functional ecological and phenotypic differentiation supports the hypothesis that this diversification is an evolutionary response to mutualism with clownfishes. Clownfishes are not merely settling in locally available hosts but recruiting to specialized host lineages with which they have co-evolved. These findings have important implications for understanding how the clownfish-sea anemone symbiosis has evolved and will shape future research agendas on this iconic model system.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"134 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147666433","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
Phylogenomics of a Genus of "Great Speciators" Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems. “大物种”属的系统基因组学揭示了岛屿系统中猖獗的不完整谱系分类、基因流动和线粒体不一致。
IF 5.7 1区 生物学
Systematic Biology Pub Date : 2026-04-03 DOI: 10.1093/sysbio/syaf075
Jenna M McCullough, Chad M Eliason, Shannon J Hackett, Corinne E Myers, Michael J Andersen
{"title":"Phylogenomics of a Genus of \"Great Speciators\" Reveals Rampant Incomplete Lineage Sorting, Gene Flow, and Mitochondrial Discordance in Island Systems.","authors":"Jenna M McCullough, Chad M Eliason, Shannon J Hackett, Corinne E Myers, Michael J Andersen","doi":"10.1093/sysbio/syaf075","DOIUrl":"10.1093/sysbio/syaf075","url":null,"abstract":"<p><p>The flora and fauna of island systems-especially those in the Indo-Pacific-are renowned for their exceptional diversification and for shaping key evolutionary theories. Yet, phylogenetic studies often undersample the full diversity of these geographic radiations. This gap stems both from the challenges of collecting single-island endemics and from the poor performance of degraded DNA when using museum specimens to infer evolutionary relationships. Advances in generating genome-wide data sets with degraded DNA from museum samples are overcoming these obstacles. Here, we leveraged whole-genome resequencing (20X average coverage) and extensive sampling of all taxonomic diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic \"Great Speciators.\" We found that four types of molecular markers (UCEs, BUSCOs, SNPs, and mtDNA) and tree-building methods did not recover a single well-supported and concordant species-level topology. Instead, we revealed pervasive incomplete lineage sorting and both ancient and contemporary gene flow, processes contribute to conflicting evolutionary histories. Complete taxonomic sampling uncovered a novel case of mitochondrial discordance between two allopatric species, consistent with a historical (but since lost) hybrid zone during successive island colonizations. Together, these results underscore how dense genomic and taxonomic sampling can reveal complex evolutionary dynamics in rapid island radiations.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"406-426"},"PeriodicalIF":5.7,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145329821","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
Correction to: Considering Decoupled Phenotypic Diversification Between Ontogenetic Phases in Macroevolution: An Example Using Triggerfishes (Balistidae). 修正:考虑宏观进化中个体发生阶段之间的解耦表型多样化:以触发鱼(Balistidae)为例。
IF 5.7 1区 生物学
Systematic Biology Pub Date : 2026-04-03 DOI: 10.1093/sysbio/syaf046
{"title":"Correction to: Considering Decoupled Phenotypic Diversification Between Ontogenetic Phases in Macroevolution: An Example Using Triggerfishes (Balistidae).","authors":"","doi":"10.1093/sysbio/syaf046","DOIUrl":"10.1093/sysbio/syaf046","url":null,"abstract":"","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"615"},"PeriodicalIF":5.7,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145606070","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
DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss. 基因重复和丢失下改进的系统基因组物种树推断。
IF 5.7 1区 生物学
Systematic Biology Pub Date : 2026-04-03 DOI: 10.1093/sysbio/syaf073
Rachel A Parsons, Mukul S Bansal
{"title":"DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss.","authors":"Rachel A Parsons, Mukul S Bansal","doi":"10.1093/sysbio/syaf073","DOIUrl":"10.1093/sysbio/syaf073","url":null,"abstract":"<p><p>Accurate species tree reconstruction in the presence of widespread gene duplication and loss is a challenging problem in eukaryote phylogenomics. Many phylogenomics methods have been developed over the years to address this challenge; these range from older methods based on gene tree parsimony to newer quartet-based methods. In this work, we introduce improved software for gene tree parsimony-based species tree reconstruction under gene duplication and loss. The new software, DupLoss-2, uses an improved procedure for computing gene losses and is far more accurate and much easier to use than its previous version released over a decade ago. We thoroughly evaluate DupLoss-2 and 8 other existing methods, including ASTRAL-Pro, ASTRAL-Pro 2, DISCO-ASTRAL, DISCO-ASTRID, FastMulRFS, and SpeciesRax, using existing benchmarking data and find that DupLoss-2 outperforms all other methods on most of the data sets. It delivers an average of almost 30% reduction in reconstruction error compared with iGTP-DupLoss, the previous version of this software, and a 10% reduction compared with the best-performing existing method. DupLoss-2 is written in C++ and is freely available open-source.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"605-614"},"PeriodicalIF":5.7,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145281029","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
Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera. 结合核与线粒体系统基因组学定义鞘翅目分类关键节点的生物信息学研究。
IF 5.7 1区 生物学
Systematic Biology Pub Date : 2026-04-03 DOI: 10.1093/sysbio/syaf031
Thomas J Creedy, Yinhuan Ding, Katherine M Gregory, Luke Swaby, Feng Zhang, Alfried P Vogler
{"title":"Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera.","authors":"Thomas J Creedy, Yinhuan Ding, Katherine M Gregory, Luke Swaby, Feng Zhang, Alfried P Vogler","doi":"10.1093/sysbio/syaf031","DOIUrl":"10.1093/sysbio/syaf031","url":null,"abstract":"<p><p>Nuclear genome sequencing for phylogenetics is resource-intensive while mitochondrial genomes can be sequenced and analyzed with relative ease for building densely sampled phylogenetic trees of the most species-rich lineages of animals. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from > 2,000 BUSCO loci mined from GenBank's Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 491 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at the family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with 3 recent nuclear phylogenomic studies resulted in the recognition of > 80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"445-467"},"PeriodicalIF":5.7,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13048007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145606012","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
Evaluating the impact and detectability of mass extinctions on total-evidence dating. 评估大灭绝对全证据定年的影响和可探测性。
IF 6.5 1区 生物学
Systematic Biology Pub Date : 2026-03-31 DOI: 10.1093/sysbio/syag032
Minghao Du,Wenhui Wang,Jingqiang Tan,Joëlle Barido-Sottani
{"title":"Evaluating the impact and detectability of mass extinctions on total-evidence dating.","authors":"Minghao Du,Wenhui Wang,Jingqiang Tan,Joëlle Barido-Sottani","doi":"10.1093/sysbio/syag032","DOIUrl":"https://doi.org/10.1093/sysbio/syag032","url":null,"abstract":"Fossils are crucial for accurately dating phylogenetic trees because their ages provide vital constraints on the timing of macroevolutionary events, and their morphological characters offer key information on evolutionary rates and phylogenetic positions. The fossilized birth-death (FBD) process is a diversification model that incorporates both extant and extinct species, serving as a tree prior that seamlessly integrates fossils into phylogenetic inference. While the FBD model can account for mass extinctions, which caused rapid, widespread organismal loss, few studies have utilized FBD models incorporating these events in phylogenetic inference. This is likely because the detectability of mass extinctions and their impact on phylogenetic inference remain unclear. Through simulations, we assessed the influence of mass extinctions on divergence time and topology inference and evaluated the detectability of mass extinction signals in total-evidence dating. We examined three FBD tree priors: without mass extinction, with known mass extinction time and survival probability, and with known mass extinction time but unknown survival probability. Our results show that the FBD model with known mass extinction time and unknown survival probability was able to reliably detect mass extinctions when they occurred, and correctly refrained from detecting mass extinctions when they were absent. Moreover different FBD models generate similar divergence time and tree topology errors. Even when the FBD model used for tree inference did not explicitly account for mass extinction events, signals of mass extinction were still detectable on the resulting MCC trees. The accuracy of the detection was similar to the one obtained from MCC trees inferred using an FBD model that includes mass extinction parameters. We also reduced the fossilization rate and the number of morphological characters, obtaining results consistent with the aforementioned findings. However, reducing the fossilization rate decreased the accuracy of detecting mass extinctions when they occurred, and reducing the number of morphological characters decreased the accuracy of divergence time inference. Furthermore, we adjusted the priors for the existence of mass extinction and the survival probability of mass extinction. We found that the prior for the existence of mass extinction had no effect on inference, whereas the prior for the survival probability of mass extinction significantly influenced both the detection of mass extinctions and the estimation of survival probabilities. It should be noted that our simulations represent a largely best-case scenario with constant diversification rates; empirical datasets with more complex evolutionary histories may present additional challenges for mass extinction detection. Finally, we applied these models to an empirical dataset of crinoids and found that, consistent with our simulation results, the inclusion of a mass extinction event in the tree prior had ","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"62 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147578213","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 of Continuous Traits on Phylogenies. 系统发育上连续性状的随机特征映射。
IF 5.7 1区 生物学
Systematic Biology Pub Date : 2026-03-31 DOI: 10.1093/sysbio/syag031
Bruce Stagg Martin, Marjorie Gail Weber
{"title":"Stochastic Character Mapping of Continuous Traits on Phylogenies.","authors":"Bruce Stagg Martin, Marjorie Gail Weber","doi":"10.1093/sysbio/syag031","DOIUrl":"https://doi.org/10.1093/sysbio/syag031","url":null,"abstract":"<p><p>Fossilized organisms only represent a small fraction of Earth's evolutionary history, motivating \"ancestral state reconstruction\" techniques for inferring unobserved phenotypes of evolving lineages based on measurements of their relatives. Stochastic character mapping has emerged as a particularly powerful approach in this regard, allowing researchers to sample histories of discrete variables on phylogenies and better account for the inherent uncertainty of reconstructed ancestral states. Here, we generalize stochastic character mapping to work with continuous variables by developing an efficient algorithm for sampling evolutionary histories under Brownian Motion models with the flexibility to include multiple correlated phenotypes, measurement error, and/or among-lineage variation in evolutionary rates/trends. We implement this \"continuous stochastic character mapping\" procedure in a new R package called contsimmap and demonstrate potential applications of this technique by developing a novel pipeline for inferring relationships between rates of continuous trait evolution and continuously-varying factors (e.g., body size, generation time)-a difficult statistical problem for which relatively few methods are available. After verifying this pipeline's performance on simulated data, we use it to show that smaller eucalypt trees tend to exhibit higher rates of flower and leaf trait evolution overall, aligning with well-established predictions based on life history theory as well as empirical patterns in other systems. Ultimately, continuous stochastic character mapping is a valuable new tool for analyzing macroevolutionary data, enabling rigorous yet flexible investigation of complex evolutionary dynamics involving continuous traits and/or continuous variables hypothesized to affect evolutionary processes.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147582501","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
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