Systematic Biology最新文献

{"title":"Global Diversity Patterns are Explained by Diversification Rates and Dispersal at Ancient, not Shallow, Timescales.","authors":"Patrick R Stephens, Maxwell J Farrell, T Jonathan Davies, John L Gittleman, Shai Meiri, Matthew O Moreira, Uri Roll, John J Wiens","doi":"10.1093/sysbio/syaf018","DOIUrl":"https://doi.org/10.1093/sysbio/syaf018","url":null,"abstract":"<p><p>Explaining global species richness patterns is a major goal of evolution, ecology, and biogeography. These richness patterns are often attributed to spatial variation in diversification rates (speciation minus extinction). Surprisingly, prominent studies of birds, fish, and plants have reported higher speciation and/or diversification rates at higher latitudes, where species richness is lower. We hypothesize that these surprising findings are explained by the focus of those studies on relatively recent macroevolutionary rates, within the last ~20 million years. Here, we analyze global richness patterns among 10,213 squamates (lizards and snakes) and explore their underlying causes. We find that when diversification rates were quantified at more recent timescales, we observed mismatched patterns of rates and richness, similar to previous studies in other taxa. Importantly, diversification rates estimated over longer timescales were instead positively related to geographic richness patterns. These observations may help resolve the paradoxical results of previous studies in other taxa. We found that diversification rates were largely unrelated to climate, even though climate and richness were related. Instead, higher tropical richness was related to ancient occupation of tropical regions, with colonization time the variable that explained the most variation in richness overall. We suggest that large-scale diversity patterns might be best understood by considering climate, deep-time diversification rates, and the time spent in different regions, rather than recent diversification rates alone. [Climate, colonization time, diversification rate, lizards, latitudinal diversity gradient, snakes, species richness].</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606110","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}

{"title":"Aquatic biotas of Sundaland are fragmented but not refugial","authors":"Erwan Delrieu-Trottin, Selim Ben Chehida, Tedjo Sukmono, Hadi Dahruddin, Arni Sholihah, Kustiati Kustiati, Yuli Fitriana, Zainal Abidin Muchlisin, Roza Elvyra, Arif Wibowo, Ilham Vemandra Utama, Ujang Nurhaman, Sopian Sauri, Renny Risdawati, Muhamad Syamsul Arifin Zein, Juliette Pouzadoux, Jean-François Agnèse, Marie-Ka Tilak, Lawrence M Page, Thomas von Rintelen, Daisy Wowor, Dirk Steinke, Stefano Mona, Lukas Rüber, Paul D N Hebert, Nicolas Hubert","doi":"10.1093/sysbio/syaf005","DOIUrl":"https://doi.org/10.1093/sysbio/syaf005","url":null,"abstract":"Tropical insular systems have long attracted biologists, stimulating some important controversies in ecology and evolution. Eustatic fluctuations during the Pleistocene have been invoked to explain species dispersal and proliferation in these fragmented systems by controlling the extent of landmasses and their temporary connections. In ancient archipelagos, the Pleistocene represents only a small slice of their history so long-standing configurations might better explain insular diversity patterns. With a geological history of ca. 30 million years, the Sunda Shelf is old. Upon entering the Pleistocene, islands of the Sunda Shelf repeatedly separated and merged; however, recent reappraisals of its paleoenvironments and evolutionary dynamics have questioned their biogeographic significance. Based on the molecular inventory of six common freshwater fish families, we explored population fragmentation and demographic history of the most common species using mitochondrial DNA sequences. Species delimitation methods, applied to 1,062 sequences belonging to 37 species from 188 sites, detected 95 Molecular Operational Taxonomic Units (MOTUs). Among the nine most widespread species, the number of MOTUs ranged from 1 to 11, and correlated with time to the most recent common ancestor. Extended Bayesian Skyline Plots applied to mitogenomes and cytochrome c oxidase I sequences detected no variation in past effective population size within MOTUs, while hierarchical Approximate Bayesian Computation provided no evidence of congruent changes in effective population sizes. Fragmentation of an ancestral range is the most likely explanation for the rampant cryptic diversity observed, but demographic inferences do not support MOTUs as being refugial from an evolutionary perspective.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"43 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546248","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}

{"title":"Phylogenomics of marine angelfishes: diagnosing sources of systematic discordance for an iconic reef fish family (F: Pomacanthidae)","authors":"Lauriane M Baraf, Julia Y Hung, Peter F Cowman","doi":"10.1093/sysbio/syaf016","DOIUrl":"https://doi.org/10.1093/sysbio/syaf016","url":null,"abstract":"Genome-scale datasets are resolving challenging nodes across the tree of life. These datasets however, characterized by inherent heterogeneity, often push traditional phylogenetic reconstruction methods to their limits. By integrating multiple phylogenomic approaches, we can identify the causes of topological discordance within genomic partitions while accounting for various sources of heterogeneity and systematic errors. Here we conduct the first in-depth analysis of discordance for the reef family Pomacanthidae (marine angelfishes) using target enrichment data of ~1,000 ultraconserved elements from 45 pomacanthid species. Our combined phylogenomic approach resolved the systematics of the family at the base of the pomacanthid tree. Despite this resolution, our analyses also highlight discordance in ancestral nodes associated with the paraphyletic Centropyge genus and monotypic Pygoplites lineage, and the impact of incomplete lineage sorting in the evolutionary history pomacanthids. Species network searches and model selection supported a reticulated evolutionary history suggesting three ancient gene flow events between ghost (or unsampled) lineages at the root of the Pomacanthidae tree and ancestors of Genicanthus, Centropyge, Chaetodontoplus and Pomacanthus lineages. This study advances our understanding of diagnosing topological discordance in genome-scale phylogenies and provide an analytical pathway for limiting systematic errors. In the process of diagnosing discordance, we identify key evolutionary processes involved in the complex evolution of marine angelfishes. While often inconvenient in phylogenetic analyses, patterns of discordance can shed light on underlying biological and evolutionary processes that shape the evolution of biodiversity.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"30 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546296","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}

{"title":"Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC","authors":"Yunheng Han, Erin K Molloy","doi":"10.1093/sysbio/syaf009","DOIUrl":"https://doi.org/10.1093/sysbio/syaf009","url":null,"abstract":"Summary methods are widely used to reconstruct species trees from gene tres while accommodating discordance from incomplete lineage sorting; however, it is increasingly recognized that their accuracy can be negatively impacted by incomplete and/or error-ridden gene trees. To address the latter, Zhang and Mirarab (2022) updated the popular summary method ASTRAL so that it weights quartets based on gene tree branch lengths and support values. The implementation of these weighting schemes presented computational challenges, leading Zhang and Mirarab (2022) to replace ASTRAL’s original algorithm (i.e., computing an exact solution within a constrained search space) in favor of search heuristics based on phylogenetic placement. Here, we show that these weighting schemes can be effectively leveraged within the Quartet Max Cut framework of Snir and Rao (2010), introducing weighted TREE-QMC. The incorporation of weighting schemes into TREE-QMC required only a small increase in time complexity compared to the unweighted algorithm; fortunately, the increase in runtime was also small, behaving more like a constant factor in our simulation study. Moreover, weighted TREE-QMC was fast and highly competitive with weighted ASTRAL, even outperforming it in terms of species tree accuracy on some challenging simulation conditions, such as large numbers of taxa. In reanalyzing two avian data sets, we found that weighting quartets by gene tree branch lengths can improve robustness to systematic homology errors and can be as effective as removing the impacted taxa from individual gene trees or removing the impacted gene trees entirely. Lastly, our study revealed that TREE-QMC was robust to extreme rates of missing taxa, suggesting its utility as a supertree method. Source code for weighted TREE-QMC is available on Github: (https://github.com/molloy-lab/TREE-QMC)","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"32 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495162","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}

{"title":"Repeated Evolution of Storage Root and Invasions of Alpine Biome Drove Replicated Radiations of the Megadiverse Corydalis (Papaveraceae) in the Qinghai-Tibet Plateau.","authors":"Huan-Wen Peng, Yuan-Yuan Ling, Kun-Li Xiang, Andrey S Erst, Xiao-Qian Li, Lian Lian, Bing Liu, Tatyana V Erst, Rosa Del C Ortiz, Florian Jabbour, Wei Wang","doi":"10.1093/sysbio/syaf014","DOIUrl":"https://doi.org/10.1093/sysbio/syaf014","url":null,"abstract":"<p><p>The interplay of key innovation and ecological opportunity is commonly recognized to be the catalyst for rapid radiation. Underground storage organs (USOs), as a vital ecological trait, are advantageous for adaptation of plants to extreme environments, but receive less attention compared to aboveground organs. Repeated evolution of various USOs has occurred across the plant tree of life. However, whether repeated occurrences of a USO in different clades of a group can promote its replicated radiations in combination with the invasion of similar environments remains poorly known. Corydalis is a megadiverse genus in Papaveraceae and exhibits remarkable variations in USO morphology and biome occupancy. Here, we first generated a robust phylogeny for Corydalis with wide taxonomic and genomic coverage based on plastome and nuclear ribosomal DNA sequence data. By dating the branching events, reconstructing ancestral ranges, evaluating diversification dynamics, and inferring evolutionary patterns of USOs and biomes and their correlations, we then tested whether the interplay of USO evolution and biome shifts has driven rapid diversification of some Corydalis lineages. Our results indicate that Corydalis began to diversify in the Qinghai-Tibet Plateau (QTP) at ca. 41 Ma, and 88% of dispersals happened through forests, suggesting that forests served as important dispersal corridors for range expansion of the genus. The storage root has originated independently at least six times in Corydalis since the Miocene, and its acquisition could have operated as a key innovation towards the adaptation to the alpine biome in the QTP. Repeated evolution of this game-changing trait and invasions of alpine biome, in combination with geoclimatic changes, could have jointly driven independent radiations of the two clades of Corydalis in the QTP at ca. 6 Ma. Our study provides new insights into the joint contribution of USO repeated evolution and biome shifts to replicated radiations, hence increasing our ability to predict evolutionary trajectories in plants facing similar environmental pressures. [Biome shift; diversification rates; Papaveraceae; phylogenomics; Qinghai-Tibet Plateau; underground storage organs.].</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459507","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}

{"title":"Recent, Intricate Speciation in Amazonia Uncovered by a Multilayered Genomic Analysis of Tree Squirrels","authors":"Edson F Abreu, Joyce R Prado, Jesús E Maldonado, Don E Wilson, Alexandre R Percequillo, Silvia E Pavan","doi":"10.1093/sysbio/syaf013","DOIUrl":"https://doi.org/10.1093/sysbio/syaf013","url":null,"abstract":"Accurate estimates of species diversity are essential for all biodiversity research. Delimiting species and understanding the underlying processes of speciation are also central components of systematic biology that frame our comprehension of the evolutionary mechanisms generating biodiversity. The South American tree squirrels (genus Guerlinguetus) are keystone mammals, widely distributed, that are critical in tree-seed predation and dispersal in one of the most fragile and threated ecosystems of the world, the tropical rainforests of South America. We obtained genomic data (ultraconserved elements and single nucleotide polymorphisms) to explore alternative hypotheses on species limits of this genus and to clarify recent and rapid speciation on continental-scale and dynamically evolving landscapes. Using a multilayered genomic approach that integrates fine-scale population genetic analyses with quantitative molecular species delimitation methods, we observed that (i) the most likely number of species within Guerlinguetus is six, contrasting with both classic morphological revision and mitochondrial species delimitation; (ii) incongruencies in species relationships still persist, which might be a response to population migration and gene flow taking place in the lowlands of eastern Amazonia and/or to the extremely rapid successive speciation events; and (iii) effective migration surfaces detected important geographic barriers associated with the major Amazonian riverine systems and the mountain ranges of the Guiana Shield. In conclusion, we uncovered unexpected and higher species diversity on Guerlinguetus and corroborate recent findings suggesting that much of the extant species-level diversity in Amazonia is young, dating back to the Quaternary. We also reinforce long-established hypotheses on the role of rivers and climate-driven forest dynamics in triggering Amazonian speciation. [gene flow; Guerlinguetus; migration; mito-nuclear discordance; Neotropics; quantitative species delimitation; Sciuridae; ultraconserved elements]","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"14 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443301","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}

{"title":"Global Patterns of Taxonomic Uncertainty and its Impacts on Biodiversity Research","authors":"Jhonny J M Guedes, Mario R Moura, Lucas Jardim, José Alexandre F Diniz-Filho","doi":"10.1093/sysbio/syaf010","DOIUrl":"https://doi.org/10.1093/sysbio/syaf010","url":null,"abstract":"Over two million species have been named so far, but many will be invalidated due to redundant descriptions. Undetected invalid species (i.e., synonyms) can impair inferences we make in biodiversity research and hamper the implementation of effective conservation strategies. However, the processes leading to the accumulation of invalid names remain largely unknown. Using multi-model inferences, we investigated the patterns and potential drivers of species- and assemblage-level variation in synonym counts across terrestrial vertebrates globally. We also explored how taxonomic uncertainty (i.e., instability in species identities) can affect latitudinal variation of diversification rates. The average number of synonyms was higher for species described earlier, better represented in scientific collections, with larger geographic ranges, occurring in temperate regions, and in areas of high biodiversity attention. In assemblage-level models, a higher average number of synonyms was associated with temperate regions harbouring more early-described species. Areas of high endemism richness showed fewer synonyms across amphibians and reptiles but had an inverse effect for birds and mammals. Other predictor-response relationships varied across taxonomic groups, biogeographical realm, and spatial grain. Assuming that more synonyms indicate more stable species that have been thoroughly studied and reviewed, high synonym numbers in temperate species and assemblages support claims of a potential latitudinal taxonomy gradient, where geographic variation in taxonomic practice could hinder the proper recognition of tropical species. We show that the accumulation of invalid names is not random and discuss how invalid hidden names can affect biodiversity inferences. A potential approach to address this problem would be developing a taxonomic uncertainty metric that could be incorporated into models (i.e., as weights to account for varying degrees of uncertainty during the fitting process). Our study provides an initial approximation and highlights the often-neglected issue of uncertainty and instability in species identities from a macroecological perspective.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"1861 3 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143417492","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}

{"title":"UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina)","authors":"Claudio G Ametrano, Jacob Jensen, H Thorsten Lumbsch, Felix Grewe","doi":"10.1093/sysbio/syaf011","DOIUrl":"https://doi.org/10.1093/sysbio/syaf011","url":null,"abstract":"The subphylum Pezizomycotina (filamentous ascomycetes) is the largest clade within Ascomycota. Despite the importance of this group of fungi, our understanding of their evolution is still limited due to insufficient taxon sampling. Although next-generation sequencing technology allows us to obtain complete genomes for phylogenetic analyses, generating complete genomes of fungal species can be challenging, especially when fungi occur in symbiotic relationships or when the DNA of rare herbarium specimens is degraded or contaminated. Additionally, assembly, annotation, and gene extraction of whole-genome sequencing data require bioinformatics skills and computational power, resulting in a substantial data burden. To overcome these obstacles, we designed a universal target enrichment probe set to reconstruct the phylogenetic relationships of filamentous ascomycetes at different phylogenetic levels. From a pool of single-copy orthologous genes extracted from available Pezizomycotina genomes, we identified the smallest subset of genetic markers that can reliably reconstruct a robust phylogeny. We used a clustering approach to identify a sequence set that could provide an optimal trade-off between potential missing data and probe set cost. We incorporated this probe set into a user-friendly wrapper script named UnFATE (https://github.com/claudioametrano/UnFATE) that allows phylogenomic inferences without requiring expert bioinformatics knowledge. In addition to phylogenetic results, the software provides a powerful multilocus alternative to ITS-based barcoding. Phylogeny and barcoding approaches can be complemented by an integrated, pre-processed, and periodically updated database of all publicly available Pezizomycotina genomes. The UnFATE pipeline, using the 195 selected marker genes, consistently performed well across various phylogenetic depths, generating trees consistent with the reference phylogenomic inferences. The topological distance between the reference trees from literature and the best tree produced by UnFATE ranged between 0.10 and 0.14 (nRF) for phylogenies from family to subphylum level. We also tested the in vitro success of the universal baits set in a target capture approach on 25 herbarium specimens from ten representative classes in Pezizomycotina, which recovered a topology congruent with recent phylogenomic inferences for this group of fungi. The discriminating power of our gene set was also assessed by the multilocus barcoding approach, which outperformed the barcoding approach based on ITS. With these tools, we aim to provide a framework for a collaborative approach to build robust, conclusive phylogenies of this important fungal clade.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"65 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143417538","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}

{"title":"The consequences of budding speciation on trees","authors":"C Tomomi Parins-Fukuchi, James G Saulsbury","doi":"10.1093/sysbio/syaf012","DOIUrl":"https://doi.org/10.1093/sysbio/syaf012","url":null,"abstract":"Paleobiologists have long sought to explain how alternative modes of speciation, including budding and bifurcating cladogenesis, shape patterns of evolution. Methods introduced over the past decade have paved the way for a renewed enthusiasm for exploring modes of speciation in the fossil record. However, the field does not yet have a strong intuition for how ancestor-descendant relationships, especially those that arise from budding speciation, might influence the shape of trees reconstructed for fossil or living clades. We developed a simulation approach based on classic paleobiological theory to ask what proportion of ancestral nodes in paleontological phylogenies are expected to correspond to sampled taxa under a range of preservational regimes. We compared our simulated results to empirical estimates of absolute fossil record completeness gathered from the literature and found that many fossilized clades of marine invertebrates are likely to display upwards of 80% sampled ancestors. Under a primarily budding model, phylogenies where 100% of the internal nodes correspond to named species are very possible for well-sampled clades at local and regional scales. We also leveraged our simulation approach to ask how budding might shape extant clades. We found that the ancestral signature of budding causes rampant hard polytomies (i.e., multifurcations), greatly impacting the shape of extant clades. Our results highlight how budding can yield dramatic and unrecognized effects on phylogenetic reconstruction of clades of both living and extinct organisms.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"65 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143417539","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}

{"title":"The Fossilized Birth-Death Model Is Identifiable.","authors":"Kate Truman, Timothy G Vaughan, Alex Gavryushkin, Alexandra Sasha Gavryushkina","doi":"10.1093/sysbio/syae058","DOIUrl":"10.1093/sysbio/syae058","url":null,"abstract":"<p><p>Time-dependent birth-death sampling models have been used in numerous studies to infer past evolutionary dynamics in different biological contexts, for example,  speciation and extinction rates in macroevolutionary studies, or effective reproductive number in epidemiological studies. These models are branching processes where lineages can bifurcate, die, or be sampled with time-dependent birth, death, and sampling rates, generating phylogenetic trees. It has been shown that in some subclasses of such models, different sets of rates can result in the same distributions of reconstructed phylogenetic trees, and therefore, the rates become unidentifiable from the trees regardless of their size. Here, we show that widely used time-dependent fossilized birth-death (FBD) models are identifiable. This subclass of models makes more realistic assumptions about the fossilization process and certain infectious disease transmission processes than the unidentifiable birth-death sampling models. Namely, FBD models assume that sampled lineages stay in the process rather than being immediately removed upon sampling. The identifiability of the time-dependent FBD model justifies using statistical methods that implement this model to infer the underlying temporal diversification or epidemiological dynamics from phylogenetic trees or directly from molecular or other comparative data. We further show that the time-dependent FBD model with an extra parameter, the removal after sampling probability, is unidentifiable. This implies that in scenarios where we do not know how sampling affects lineages, we are unable to infer this extra parameter together with birth, death, and sampling rates solely from trees.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"112-123"},"PeriodicalIF":6.1,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11997801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142475252","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}