Systematic Biology最新文献

{"title":"But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating","authors":"Nicolás Mongiardino Koch, Jeffrey R Thompson, Rich Mooi, Greg W Rouse","doi":"10.1093/sysbio/syaf055","DOIUrl":"https://doi.org/10.1093/sysbio/syaf055","url":null,"abstract":"Phylogenetic clock models translate inferred amounts of evolutionary change (calculated from either genotypes or phenotypes) into estimates of elapsed time, providing a mechanism for time scaling phylogenetic trees. Relaxed-clock models, which accommodate variation in evolutionary rates across branches, are one of the main components of Bayesian dating, yet their consequences for total-evidence phylogenetics have not been thoroughly explored. Here, we combine morphological, molecular (both transcriptomic and Sanger-sequenced), and stratigraphic datasets for all major lineages of echinoids (sea urchins, heart urchins, sand dollars). We then perform total-evidence dated inference under the fossilized birth-death prior, varying two analytical conditions: the choice between autocorrelated and uncorrelated relaxed clocks, which enforce (or not) evolutionary rate inheritance; and the ability to recover fossil terminals as direct ancestors. Our results highlight a previously unnoticed interaction between tree and clock models, with analyses implementing an autocorrelated clock failing to recover any direct ancestors. Nonetheless, even under conditions conducive to the placement of fossil terminals as ancestors, we find this type of relationship to be accommodated without any impact on either topology or node ages. On the other hand, tree topology, fossil placement, divergence times, and downstream macroevolutionary inferences (e.g., ancestral state reconstructions) were all strongly affected by the type of relaxed clock implemented. In regions of the tree where molecular rate variation is pervasive and morphological signal relatively uninformative, fossil tips seem to play little to no role in informing divergence times, and instead passively move in and out of clades depending on the ages imposed upon surrounding nodes by molecular data. Our results highlight the extent to which the phylogenetic and macroevolutionary conclusions of total-evidence dated analyses are contingent on the choice of relaxed-clock model, highlighting the need for either careful methodological validation or a thorough assessment of sensitivity. Our efforts continue to illuminate the echinoid tree of life, supporting the erection of the order Apatopygoida to include three living species last sharing a common ancestor with other extant lineages around the time of the Jurassic-Cretaceous boundary. Furthermore, they also illustrate how the phylogenetic placement of extinct clades hinges upon the modelling of molecular data, evidencing the extent to which the fossil record remains subservient to phylogenomics.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"12 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825112","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":"Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression and Demographic Analyses of Asian Shrew Moles.","authors":"Yi-Xian Li,Zhong-Zheng Chen,Quan Li,Tao Zhang,Feng Cheng,Wen-Yu Song,Xue-You Li,Shui-Wang He,Hong-Jiao Wang,Kenneth Otieno Onditi,Xue-Long Jiang","doi":"10.1093/sysbio/syaf052","DOIUrl":"https://doi.org/10.1093/sysbio/syaf052","url":null,"abstract":"The Mountains of Southwest China, a global biodiversity hotspot, have a unique \"sky island\" landscape with high diversity of both ancient and recent-formed species. While their distribution patterns offer significant insights into diversification processes, the complex geological and climatic history, combined with dynamic histories of gene flow in endemic taxa, make unravelling this history challenging. This study focuses on Asian shrew moles (genus Uropsilus), an ancient group endemic to this region with an unresolved taxonomic system. By combining phylogenomic, introgression and demographic history analyses, we investigated the historical patterns of species diversification in this genus. We detected phylogenetic discordances among rapidly diverged lineages, driven by incomplete lineage sorting, both recent and ancient gene flow, and ghost introgression. The gene flow patterns revealed strong genetic isolation in the Hengduan Mountains region, contrasted by more extensive dispersal or connectivity in areas to its east, while suggesting potential ring-like diversification around the Sichuan Basin. Demographic history indicated that rapidly diverged lineages south of the Yangtze River exhibited significantly different responses to climatic fluctuations compared to other lineages, with the East Asian monsoon likely driving their radiative differentiation and dispersal. Our study demonstrates the impacts of mountain uplift, climatic changes, and the connectivity of sky island refugia in shaping the diverse patterns of species differentiation and their distribution. [phylogenomics; introgression; Asian shrew moles; demographic history].","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"96 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144748115","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 climate cooling spurred skipper butterfly diversification","authors":"Emmanuel F A Toussaint, Fabien L Condamine, Ana Paula dos Santos De Carvalho, David M Plotkin, Emily A Ellis, Kelly M Dexter, Chandra Earl, Kwaku Aduse-Poku, Michael F Braby, Hideyuki Chiba, Riley J Gott, Kiyoshi Maruyama, Ana BB Morais, Chris J Müller, Djunijanti Peggie, Szabolcs Sáfián, Roger Vila, Andrew D Warren, Masaya Yago, Jesse W Breinholt, Marianne Espeland, Naomi E Pierce, David J Lohman, Akito Y Kawahara","doi":"10.1093/sysbio/syaf029","DOIUrl":"https://doi.org/10.1093/sysbio/syaf029","url":null,"abstract":"Characterizing drivers governing the diversification of species-rich lineages is challenging. Although butterflies are one of the most well-studied groups of insects, there are few comprehensive studies investigating their diversification dynamics. Here, we reconstruct a phylogenomic tree for ca. 1,500 species in the family Hesperiidae, the skippers, to test whether historical global climate change, geographical range evolution, and host-plant association are drivers of diversification. Our findings suggest skippers originated in Laurasia before the Cretaceous-Paleogene mass extinction, in a northern region centered on Beringia before colonizing southern regions coinciding with global climate cooling. Climate cooling also fostered the diversification of skippers throughout the Cenozoic possibly by fueling biome transitions from closed to open ecosystems such as grasslands. An early shift from dicot-feeding to monocot-feeding reduced extinction rates and increased speciation rates, explaining the large diversity of grass-feeding adapted skippers. A dynamic geographic range evolution and host-plant shifts linked with long-term climate change explain skipper butterfly diversification.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"86 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715356","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":"Phylogenetic Analysis of Characters with Dependencies under Maximum Likelihood","authors":"Pablo A Goloboff","doi":"10.1093/sysbio/syaf051","DOIUrl":"https://doi.org/10.1093/sysbio/syaf051","url":null,"abstract":"The dependencies between characters used in phylogenetic analysis (e.g., inapplicabilities, functional dependencies) can be taken into account by using combinations of character states as possible ancestral morphotypes, and using appropriate rates of transformation between such morphotypes. As every morphotype represents a permissible combination of the original character states, this allows easily ruling out specific combinations of character states, and taking into account changes that are either less or more likely to co-occur, or to occur in certain contexts. For inapplicable characters, Goloboff et al. (2021) used morphotypes but proposed obtaining transition probabilities between morphotypes from products of transition probabilities of the original characters and factors to incorporate dependencies. The product of transition probabilities is shown here to be flawed (failing the time-continuity requirement of phylogenetic Markov models, essential for statistical consistency under the model). Tarasov (2023) used the same delimitation of morphotypes but proposed obtaining transition probabilities from rate matrices, synthesized in a stepwise fashion from the hierarchy of dependencies. This paper shows that the rate matrices can easily be created, instead of with a stepwise synthesis, from direct comparisons between legitimate morphotypes (as done by Goloboff and De Laet 2023 for parsimony). Based on a few simple rules, the resulting rate matrices are (for inapplicable characters) identical to those obtained by Tarasov (2023). Additionally, in the computer program TNT, biological dependencies beyond mere inapplicability can be specified by the user with a simple syntax for (combinations of) states in “parent” characters restricting the states that “child” characters can take, using AND and OR conjunctions for elaborate interactions. These researcher-defined rules are used to internally convert the original characters into morphotypes, discarding morphotypes made impossible by the rules. In the case of biological dependencies (where, depending on the parent characters, there can be restrictions in the states that dependent characters can take, instead of the character being inapplicable), the rates of transition between morphotypes cannot be calculated solely from comparisons of states differing in both morphotypes –consideration of the conditions of dependency is needed as well.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"118 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144710791","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":"Correction to: How Important Is Budding Speciation for Comparative Studies?","authors":"","doi":"10.1093/sysbio/syaf042","DOIUrl":"https://doi.org/10.1093/sysbio/syaf042","url":null,"abstract":"","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"25 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684207","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":"PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks.","authors":"Louxin Zhang, Banu Cetinkaya, Daniel H Huson","doi":"10.1093/sysbio/syaf049","DOIUrl":"https://doi.org/10.1093/sysbio/syaf049","url":null,"abstract":"<p><p>Unrooted phylogenetic networks are commonly used to represent evolutionary data in the presence of incompatibilities. While rooted phylogenetic networks offer a more explicit framework for depicting evolutionary histories involving reticulate events, they are reported less frequently, probably due to a lack of tools that are as easily applicable as those for unrooted networks. Here, we introduce PhyloFusion, a fast and user-friendly method for constructing rooted phylogenetic networks from sets of rooted phylogenetic trees. The resulting networks have the tree-child property. The algorithm accommodates trees with unresolved nodes -often resulting from the contraction of low-support edges- as well as some degree of missing taxa. We demonstrate its application to the analysis of functionally related gene groups and show that it can efficiently handle datasets comprising tens of trees or hundreds of taxa. An open source implementation of PhyloFusion is available as part of the SplitsTree app: https://www.github.com/husonlab/splitstree6 All data available here: https://doi.org/10.5061/dryad.k3j9kd5h5.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144650538","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":"Correction to: Global Patterns of Taxonomic Uncertainty and its Impacts on Biodiversity Research.","authors":"","doi":"10.1093/sysbio/syaf045","DOIUrl":"https://doi.org/10.1093/sysbio/syaf045","url":null,"abstract":"","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"108 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630471","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":"Revisiting the Multispecies Coalescent Model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae).","authors":"Joaquín Villamil,Mariana Morando,Luciano J Avila,Flávia M Lanna,Emanuel M Fonseca,Jack W Sites,Arley Camargo","doi":"10.1093/sysbio/syaf048","DOIUrl":"https://doi.org/10.1093/sysbio/syaf048","url":null,"abstract":"Departures from the Multispecies Coalescent (MSC) assumptions could cause artefactual topologies and node height estimates, and therefore, trees inferred without MSC model fit testing could potentially misrepresent an accurate approximation of the evolutionary history of a group. The current implementation of MSC model testing for non-genomic level molecular markers cannot process trees estimated from BEAST 2, limiting its application for large datasets of sequence-based markers. Here we recode functions of the R package P2C2M to assess model fit to the MSC and apply this new implementation, which we named P2C2M2, to test the MSC model in a 16-loci dataset of 42 lizard species focused on the Liolaemus wiegmannii group. We found strong evidence of model departures in several loci, possibly due to historical gene flow, which could also be causing an unexpected position of the L. wiegmannii group within the L. montanus section of Eulaemus, when hybridization is not accounted for. The L. anomalus group is inferred as the closest to the L. wiegmannii group when gene flow is incorporated via a Multispecies Network Coalescent model, and a reticulation, suggesting historical gene flow between the L. wiegmannii and L. montanus groups is inferred, which has not been previously reported. We argue that there are at least three sources of discrepancy between the literature and the node ages estimated in our study: the use of strict molecular clocks without statistical justification, misplaced fossil calibrations, and the estimation of coalescent times instead of species divergence times. We encouraged systematists to routinely test the fit of the MSC model when estimating species trees using sequence-based markers, and to follow a phylogenetic network approach when both this test is significant and when historical gene flow is considered one plausible source of the departure from the MSC model.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"697 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144594356","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":"torchtree: flexible phylogenetic model development and inference using PyTorch.","authors":"Mathieu Fourment, Matthew Macaulay, Christiaan J Swanepoel, Xiang Ji, Marc A Suchard, Frederick A Matsen Iv","doi":"10.1093/sysbio/syaf047","DOIUrl":"https://doi.org/10.1093/sysbio/syaf047","url":null,"abstract":"<p><p>Bayesian inference has predominantly relied on the Markov chain Monte Carlo (MCMC) algorithm for many years. However, MCMC is computationally laborious, especially for complex phylogenetic models of time trees. This bottleneck has led to the search for alternatives, such as variational Bayes, which can scale better to large datasets. In this paper, we introduce torchtree, a framework written in Python that allows developers to easily implement rich phylogenetic models and algorithms using a fixed tree topology. One can either use automatic differentiation, or leverage torchtree's plug-in system to compute gradients analytically for model components for which automatic differentiation is slow. We demonstrate that the torchtree variational inference framework performs similarly to BEAST in terms of speed, and delivers promising approximation results, though accuracy varies across scenarios. Furthermore, we explore the use of the forward KL divergence as an optimizing criterion for variational inference, which can handle discontinuous and non-differentiable models. Our experiments show that inference using the forward KL divergence is frequently faster per iteration compared to the evidence lower bound (ELBO) criterion, although the ELBO-based inference may converge faster in some cases. Overall, torchtree provides a flexible and efficient framework for phylogenetic model development and inference using PyTorch. phylogenetics, Bayesian inference, variational Bayes, PyTorch.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561212","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":"Coping with Ineffective Overlap in Multilocus Phylogenetics.","authors":"Ana Serra Silva, Karen Siu-Ting, Christopher J Creevey, Davide Pisani, Mark Wilkinson","doi":"10.1093/sysbio/syaf044","DOIUrl":"https://doi.org/10.1093/sysbio/syaf044","url":null,"abstract":"<p><p>Missing data is a long standing issue in phylogenetic inference, which often results in high levels of taxonomic instability, obscuring otherwise well supported relationships. Multiple approaches have been developed to deal with the negative effects of ineffective overlap on tree resolution, often by identifying taxa for removal. Here we repurpose a heuristic method developed to identify unstable taxa in morphological data matrices, concatabominations, and combine it with a novel gene-tree jackknifing on matrix representation of trees to identify candidates for targeted sequencing. Using a multilocus caecilian dataset we illustrate the method's capacity to identify candidate taxa and loci for additional sequencing, compare the results to those of the mathematics-based gene sampling sufficiency approach and explore the terrace space associated with the multilocus dataset. We show that our approach yields tractable numbers of loci/taxa for targeted sequencing that successfully mitigate topological instability due to ineffective overlap, even when modest amounts of data are added.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561211","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}