Phylogenetic inference typically assumes that the data has evolved under Stationary, Reversible and Homogeneous (SRH) conditions. Many empirical and simulation studies have shown that assuming SRH conditions can lead to significant errors in phylogenetic inference when the data violates these assumptions. Yet, many simulation studies focused on extreme non-SRH conditions that represent worst-case scenarios and not the average empirical dataset. In this study, we simulate datasets under various degrees of non-SRH conditions using empirically derived parameters to mimic real data and examine the effects of incorrectly assuming SRH conditions on inferring phylogenies. Our results show that maximum likelihood inference is generally quite robust to a wide range of SRH model violations but is inaccurate under extreme convergent evolution. [Phylogenetic inference, model violations, systematic bias, simulations, evolution under non-SRH conditions]
{"title":"Phylogenetic Accuracy Under Non-Stationary and Non-Homogeneous Conditions: A Simulation Study","authors":"Suha Naser-Khdour, Bui Quang Minh, Robert Lanfear","doi":"10.1093/sysbio/syag010","DOIUrl":"https://doi.org/10.1093/sysbio/syag010","url":null,"abstract":"Phylogenetic inference typically assumes that the data has evolved under Stationary, Reversible and Homogeneous (SRH) conditions. Many empirical and simulation studies have shown that assuming SRH conditions can lead to significant errors in phylogenetic inference when the data violates these assumptions. Yet, many simulation studies focused on extreme non-SRH conditions that represent worst-case scenarios and not the average empirical dataset. In this study, we simulate datasets under various degrees of non-SRH conditions using empirically derived parameters to mimic real data and examine the effects of incorrectly assuming SRH conditions on inferring phylogenies. Our results show that maximum likelihood inference is generally quite robust to a wide range of SRH model violations but is inaccurate under extreme convergent evolution. [Phylogenetic inference, model violations, systematic bias, simulations, evolution under non-SRH conditions]","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"30 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122078","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}
Hybridization involving extinct or unsampled ("ghost") lineages profoundly influences species’ evolutionary histories, but detecting such introgression remains methodologically challenging. We introduce D-BPP, a framework that integrates the heuristic D-statistic (or ABBA-BABA test) with Bayesian phylogenomic inference (implemented in BPP) to efficiently infer phylogenetic networks. In D-BPP, we first employ the D-statistic to rapidly identify candidate introgression events on a predefined bifurcating species tree; then we leverage the Bayesian test in BPP to rigorously validate these candidates and sequentially add them to the species tree, retaining only those events with strong statistical support. When the species tree is ambiguous, D-BPP identifies the most probable topology by comparing introgression models in a Bayesian framework. Through dedicated simulation analyses, we show that the D-BPP workflow has high power: the D-statistic reliably detects the presence of introgression, BPP accurately discriminates among alternative introgression scenarios, and the key procedural steps of the pipeline are empirically well-justified. Critically, our framework excels at detecting ghost introgression, which is often unidentifiable or overlooked by existing methods—whether heuristic or full-likelihood. Applied to genomic datasets from Panthera (big cats) and Thuja (conifers), D-BPP uncovered previously undetected ghost introgression events in both clades, underscoring the pervasive role ghost lineages have played across diverse taxa. By combining the computational efficiency of heuristic D-statistics with the robust statistical rigor of full-likelihood Bayesian inference, D-BPP provides a practical and powerful approach for reconstructing complex reticulate evolutionary histories.
{"title":"Synergizing Bayesian and Heuristic Approaches: D-BPP Uncovers Ghost Introgression in Panthera and Thuja","authors":"Yang Yang, Xiao-Xu Pang, Ya-Mei Ding, Bo-Wen Zhang, Wei-Ning Bai, Da-Yong Zhang","doi":"10.1093/sysbio/syag012","DOIUrl":"https://doi.org/10.1093/sysbio/syag012","url":null,"abstract":"Hybridization involving extinct or unsampled (\"ghost\") lineages profoundly influences species’ evolutionary histories, but detecting such introgression remains methodologically challenging. We introduce D-BPP, a framework that integrates the heuristic D-statistic (or ABBA-BABA test) with Bayesian phylogenomic inference (implemented in BPP) to efficiently infer phylogenetic networks. In D-BPP, we first employ the D-statistic to rapidly identify candidate introgression events on a predefined bifurcating species tree; then we leverage the Bayesian test in BPP to rigorously validate these candidates and sequentially add them to the species tree, retaining only those events with strong statistical support. When the species tree is ambiguous, D-BPP identifies the most probable topology by comparing introgression models in a Bayesian framework. Through dedicated simulation analyses, we show that the D-BPP workflow has high power: the D-statistic reliably detects the presence of introgression, BPP accurately discriminates among alternative introgression scenarios, and the key procedural steps of the pipeline are empirically well-justified. Critically, our framework excels at detecting ghost introgression, which is often unidentifiable or overlooked by existing methods—whether heuristic or full-likelihood. Applied to genomic datasets from Panthera (big cats) and Thuja (conifers), D-BPP uncovered previously undetected ghost introgression events in both clades, underscoring the pervasive role ghost lineages have played across diverse taxa. By combining the computational efficiency of heuristic D-statistics with the robust statistical rigor of full-likelihood Bayesian inference, D-BPP provides a practical and powerful approach for reconstructing complex reticulate evolutionary histories.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"56 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146122040","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}
Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fundamentally caused by large amounts of independent change along branches, causing the model to be unable to distinguish phylogenetic signal from noise. The Dayhoff Exchange Score (DE-score) is a new metric to assess this form of site saturation within and between amino acid datasets, which provides both a whole dataset overview and taxon-specific values that represent the contribution of a given taxon to the whole dataset entropic site saturation. We first assess the efficacy of this score at detecting increased entropic site saturation on over 20,000 simulation datasets, compare it to the existing Slope R2 score and then assess its efficacy in the face of the potentially confounding factors of increasing taxon number, number of positions in the alignment, missing data and noise. Finally, we use the DE-Score to re-evaluate several previously published datasets, to illustrate its efficacy. The DE-Score is available at: https://github.com/JFFleming/DEScore
{"title":"The Dayhoff Exchange Score: A new metric to quantify entropic site saturation in amino acid datasets prior to phylogenetic analysis","authors":"James F Fleming, Torsten Hugo Struck","doi":"10.1093/sysbio/syag009","DOIUrl":"https://doi.org/10.1093/sysbio/syag009","url":null,"abstract":"Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fundamentally caused by large amounts of independent change along branches, causing the model to be unable to distinguish phylogenetic signal from noise. The Dayhoff Exchange Score (DE-score) is a new metric to assess this form of site saturation within and between amino acid datasets, which provides both a whole dataset overview and taxon-specific values that represent the contribution of a given taxon to the whole dataset entropic site saturation. We first assess the efficacy of this score at detecting increased entropic site saturation on over 20,000 simulation datasets, compare it to the existing Slope R2 score and then assess its efficacy in the face of the potentially confounding factors of increasing taxon number, number of positions in the alignment, missing data and noise. Finally, we use the DE-Score to re-evaluate several previously published datasets, to illustrate its efficacy. The DE-Score is available at: https://github.com/JFFleming/DEScore","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"57 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146071531","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}
Traditionally, the inference of species trees has relied on orthologs, or genes related through speciation events, to the exclusion of paralogs, or genes related through duplication events. This has led to a focus on using only gene families with a single gene-copy per species, as these families are likely to be composed of orthologs. However, recent work has demonstrated that phylogenetic inference using paralogs is both accurate and allows researchers to take advantage of more data. Here, we investigate a case in which using larger gene families actually increases accuracy compared to using single-copy genes alone. Long-branch attraction is a phenomenon in which taxa with long branches may be incorrectly inferred as sister taxa due to homoplasy. The most common solution to long-branch attraction is to increase taxon sampling to break up long branches. Sampling additional taxa is not always feasible, possibly due to extinction or limited access to high-quality DNA. We propose the use of larger gene families with additional gene copies to break up long branches. Using simulations, we demonstrate that using larger gene families mitigates the impacts of long-branch attraction across large regions of parameter space, especially when either maximum parsimony or maximum likelihood with a misspecified substitution model is used for inference. We also analyze data from Chelicerates, with a focus on assessing support for a sister relationship between scorpions and pseudoscorpions. Previous work has suggested that the failure to recover this relationship is due to long-branch attraction between pseudoscorpions and other lineages. Using data from larger gene families increases support for a clade uniting scorpions and pseudoscorpions, although other resolutions of this relationship continue to have higher support. Together, this work highlights the potential utility of larger gene families in phylogenetic inference.
{"title":"Using gene trees with lineage-specific duplicates for phylogenetic inference mitigates the effects of long-branch attraction.","authors":"Megan L Smith,Matthew W Hahn","doi":"10.1093/sysbio/syaf089","DOIUrl":"https://doi.org/10.1093/sysbio/syaf089","url":null,"abstract":"Traditionally, the inference of species trees has relied on orthologs, or genes related through speciation events, to the exclusion of paralogs, or genes related through duplication events. This has led to a focus on using only gene families with a single gene-copy per species, as these families are likely to be composed of orthologs. However, recent work has demonstrated that phylogenetic inference using paralogs is both accurate and allows researchers to take advantage of more data. Here, we investigate a case in which using larger gene families actually increases accuracy compared to using single-copy genes alone. Long-branch attraction is a phenomenon in which taxa with long branches may be incorrectly inferred as sister taxa due to homoplasy. The most common solution to long-branch attraction is to increase taxon sampling to break up long branches. Sampling additional taxa is not always feasible, possibly due to extinction or limited access to high-quality DNA. We propose the use of larger gene families with additional gene copies to break up long branches. Using simulations, we demonstrate that using larger gene families mitigates the impacts of long-branch attraction across large regions of parameter space, especially when either maximum parsimony or maximum likelihood with a misspecified substitution model is used for inference. We also analyze data from Chelicerates, with a focus on assessing support for a sister relationship between scorpions and pseudoscorpions. Previous work has suggested that the failure to recover this relationship is due to long-branch attraction between pseudoscorpions and other lineages. Using data from larger gene families increases support for a clade uniting scorpions and pseudoscorpions, although other resolutions of this relationship continue to have higher support. Together, this work highlights the potential utility of larger gene families in phylogenetic inference.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"18 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146056863","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}
Li-Na Sha, Hao Yan, Cao Deng, Fan Yang, Ze-Hou Liu, Jun Li, Yue Zhang, Yi-Ran Cheng, Dan-Dan Wu, Yi Wang, Hou-Yang Kang, Hai-Qin Zhang, Gen-Lou Sun, Yu-Hu Shen, Yong-Hong Zhou, Wu-Yun Yang, Xing Fan
The wheat tribe Triticeae, widely known for its economic importance, is a species-diverse and polyploid-rich group in Poaceae. However, despite decades of intensive efforts, the phylogenetic relationships, genome origins, and diversification dynamics of Triticeae species remain uncertain. Here, we infer the phylogenetic and diversification patterns of Triticeae using 1,546 nuclear genes from 164 transcriptomes/genomes that represent ∼83% of the recognized genera. Our phylogeny provides robust and well-supported estimates of the relationships among diploids and polyploids, which will be indispensable for studying biodiversity and breeding innovative germplasms. Diversification dynamic analysis suggests that Triticeae has undergone continuous evolutionary diversification to varying degrees since its origin during the Miocene, with acceleration in the St-ortholog lineages, indicating asymmetric diversification patterns among the homoeologous lineages in the St-genome-containing polyploid radiation. Multiple factors, including extinct donors and nonreciprocal recombination, complicated the origin of the B and G genomes of wheat and the Y and Xm genomes of wheatgrass. Asymmetric polyploidization and mixed-ploidy introgression might have constituted an evolutionary impetus driving rapid radiation and hyperdiversity of the St-genome-containing polyploid species in Triticeae. Our results provide new insights into the evolutionary origins of Triticeae that could promote the study of other rapidly radiated lineages in terms of polyploid origin and diversification processes.
{"title":"Phylotranscriptomic analyses uncover the evolutionary history and asymmetric diversification patterns of the wheat tribe.","authors":"Li-Na Sha, Hao Yan, Cao Deng, Fan Yang, Ze-Hou Liu, Jun Li, Yue Zhang, Yi-Ran Cheng, Dan-Dan Wu, Yi Wang, Hou-Yang Kang, Hai-Qin Zhang, Gen-Lou Sun, Yu-Hu Shen, Yong-Hong Zhou, Wu-Yun Yang, Xing Fan","doi":"10.1093/sysbio/syag008","DOIUrl":"https://doi.org/10.1093/sysbio/syag008","url":null,"abstract":"<p><p>The wheat tribe Triticeae, widely known for its economic importance, is a species-diverse and polyploid-rich group in Poaceae. However, despite decades of intensive efforts, the phylogenetic relationships, genome origins, and diversification dynamics of Triticeae species remain uncertain. Here, we infer the phylogenetic and diversification patterns of Triticeae using 1,546 nuclear genes from 164 transcriptomes/genomes that represent ∼83% of the recognized genera. Our phylogeny provides robust and well-supported estimates of the relationships among diploids and polyploids, which will be indispensable for studying biodiversity and breeding innovative germplasms. Diversification dynamic analysis suggests that Triticeae has undergone continuous evolutionary diversification to varying degrees since its origin during the Miocene, with acceleration in the St-ortholog lineages, indicating asymmetric diversification patterns among the homoeologous lineages in the St-genome-containing polyploid radiation. Multiple factors, including extinct donors and nonreciprocal recombination, complicated the origin of the B and G genomes of wheat and the Y and Xm genomes of wheatgrass. Asymmetric polyploidization and mixed-ploidy introgression might have constituted an evolutionary impetus driving rapid radiation and hyperdiversity of the St-genome-containing polyploid species in Triticeae. Our results provide new insights into the evolutionary origins of Triticeae that could promote the study of other rapidly radiated lineages in terms of polyploid origin and diversification processes.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053714","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}
Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.
{"title":"Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of homologous gene copies from target enrichment data.","authors":"Nora Walden, Christiane Kiefer, Marcus A Koch","doi":"10.1093/sysbio/syag007","DOIUrl":"https://doi.org/10.1093/sysbio/syag007","url":null,"abstract":"<p><p>Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2026-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053728","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}
Sebastian Höhna,William A Freyman,Zachary Nolen,John P Huelsenbeck,Michael R May,Bruce Rannala,Brian R Moore
Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model-called the birth-death-shift (BDS) process-in which diversification rates may vary across both extant and extinct and unsampled lineages. We estimate the parameters of this model in a Bayesian statistical framework from phylogenies of exclusively extant lineages. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical primates dataset, which reveal that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a statistically coherent model.
{"title":"Inferring branch-specific rates of lineage diversification under the birth-death-shift process.","authors":"Sebastian Höhna,William A Freyman,Zachary Nolen,John P Huelsenbeck,Michael R May,Bruce Rannala,Brian R Moore","doi":"10.1093/sysbio/syag003","DOIUrl":"https://doi.org/10.1093/sysbio/syag003","url":null,"abstract":"Inferring how rates of speciation and extinction vary across lineages has proven to be a difficult statistical problem. Here we describe a stochastic-diversification model-called the birth-death-shift (BDS) process-in which diversification rates may vary across both extant and extinct and unsampled lineages. We estimate the parameters of this model in a Bayesian statistical framework from phylogenies of exclusively extant lineages. We perform simulation studies to validate the implementation of our method and to characterize its statistical behavior. We also perform analyses of an empirical primates dataset, which reveal that estimates of branch-specific diversification rates are robust to the assumed prior distribution on the number of diversification-rate shifts. Our implementation of the BDS model in RevBayes provides biologists with a flexible approach for estimating branch-specific diversification rates under a statistically coherent model.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"42 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146033845","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}
Lacie G Newton,John C Abbott,Seth M Bybee,Payton Carter,Paul B Frandsen,Aaron Goodman,Robert Guralnick,Brittney Hahn,Jacob Idec,Vincent J Kalkman,Manpreet Kolhi,Judicaël Fomekong-Lontchi,Pungki Lupiyanigdyah,Violet Onsongo,Emma Rowe,Melissa Sanchez-Herrera,Stefan Pinkert,Laura Sutherland,Ethan Tolman,Rhema Uche-Dike,Phil Barden,Michael Belitz,Cornelio A Bota-Sierra,Adolfo Cordero-Rivera,Alex Córdoba-Aguilar,Klaas-Douwe B Dijkstra,Rory A Dow,Juliana Ehlert,Rhainer G Ferreira,Matti Hämäläinen,Leandro Juen,M Olalla Lorenzo-Carballa,Bill Mauffray,Anne L Nielsen,Pablo Pessacq,Thai Hong Pham,Ângelo Parise Pinto,Stephen J Richards,Ruth Salas,Jeffrey H Skevington,Gunther Theischinger,Haomiao Zhang,Jessica L Ware
Dragonflies and damselflies (Insecta: Odonata) are descended from what were most likely the first winged animals, which flew ∼320 million years ago (Ma). They comprise ∼6400 extant species distributed across all continents except Antarctica. Examination of long-standing hypotheses regarding the role of flight behavior and wing morphology in shaping the global distribution of odonates has been limited by spatial and taxonomic scope. Here we leverage mobilized trait and distribution data derived from specimens and literature combined with a uniquely comprehensive target-enriched phylogeny (∼940 loci) covering all families and 67% of recognized genera. Ancestral state reconstruction of flight behavior strategies ("flyer" vs. "percher") suggests the odonate ancestor was a flyer, spending a majority of its time when active on the wing, with multiple independent transitions to percher. Several transitions back to the flyer behavior have also occurred. Aspect ratios for forewings and hindwings showed a strong relationship between these traits and perching and flying behavioral strategies. Divergence time estimation suggests the crown age of Odonata to be 290-325 Ma. Bayesian biogeographical evolutionary analysis of nine biogeographical realms provides a preliminary biogeographical history for odonates spanning 325 Ma. Key family-level splits occurred during the Jurassic and Cretaceous, paralleling the increasing isolation of landmasses and the poleward drift of the contemporary Australasian and Holarctic regions. Both behavioral and morphological adaptations likely facilitated the distributional success of select odonate lineages. This study lays the foundation for a revised classification of odonates and a more complete understanding of the influence of flight behavior and wing morphology in relation to evolutionary processes shaping past and current odonate diversity.
{"title":"Soaring Systematics: an evaluation of biogeography and flight behavior in dragonflies and damselflies (Insecta: Odonata) using phylogenomics.","authors":"Lacie G Newton,John C Abbott,Seth M Bybee,Payton Carter,Paul B Frandsen,Aaron Goodman,Robert Guralnick,Brittney Hahn,Jacob Idec,Vincent J Kalkman,Manpreet Kolhi,Judicaël Fomekong-Lontchi,Pungki Lupiyanigdyah,Violet Onsongo,Emma Rowe,Melissa Sanchez-Herrera,Stefan Pinkert,Laura Sutherland,Ethan Tolman,Rhema Uche-Dike,Phil Barden,Michael Belitz,Cornelio A Bota-Sierra,Adolfo Cordero-Rivera,Alex Córdoba-Aguilar,Klaas-Douwe B Dijkstra,Rory A Dow,Juliana Ehlert,Rhainer G Ferreira,Matti Hämäläinen,Leandro Juen,M Olalla Lorenzo-Carballa,Bill Mauffray,Anne L Nielsen,Pablo Pessacq,Thai Hong Pham,Ângelo Parise Pinto,Stephen J Richards,Ruth Salas,Jeffrey H Skevington,Gunther Theischinger,Haomiao Zhang,Jessica L Ware","doi":"10.1093/sysbio/syag005","DOIUrl":"https://doi.org/10.1093/sysbio/syag005","url":null,"abstract":"Dragonflies and damselflies (Insecta: Odonata) are descended from what were most likely the first winged animals, which flew ∼320 million years ago (Ma). They comprise ∼6400 extant species distributed across all continents except Antarctica. Examination of long-standing hypotheses regarding the role of flight behavior and wing morphology in shaping the global distribution of odonates has been limited by spatial and taxonomic scope. Here we leverage mobilized trait and distribution data derived from specimens and literature combined with a uniquely comprehensive target-enriched phylogeny (∼940 loci) covering all families and 67% of recognized genera. Ancestral state reconstruction of flight behavior strategies (\"flyer\" vs. \"percher\") suggests the odonate ancestor was a flyer, spending a majority of its time when active on the wing, with multiple independent transitions to percher. Several transitions back to the flyer behavior have also occurred. Aspect ratios for forewings and hindwings showed a strong relationship between these traits and perching and flying behavioral strategies. Divergence time estimation suggests the crown age of Odonata to be 290-325 Ma. Bayesian biogeographical evolutionary analysis of nine biogeographical realms provides a preliminary biogeographical history for odonates spanning 325 Ma. Key family-level splits occurred during the Jurassic and Cretaceous, paralleling the increasing isolation of landmasses and the poleward drift of the contemporary Australasian and Holarctic regions. Both behavioral and morphological adaptations likely facilitated the distributional success of select odonate lineages. This study lays the foundation for a revised classification of odonates and a more complete understanding of the influence of flight behavior and wing morphology in relation to evolutionary processes shaping past and current odonate diversity.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"64 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146015242","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}
Rapid species radiations make hybridization among species more likely. Detecting and reconstructing hybridization is therefore critical for understanding species relationships in many cases. We explored the relative performance of two phylogenetic network methods, SNaQ, a gene tree-based method, and PhyNEST, a site pattern-based method, in evaluating the plausibility of proposed past hybridization hypotheses. As our study system, we used the New Zealand cicada genera Kikihia and Maoricicada. Previous phylogenomic work on these two species radiations suggested multiple hybridization events in response to changing landscapes and climate. We generated hypotheses for specific hybridization events based on observed hybrid mating songs and patterns of mito-nuclear discordance from previous studies. We tested our hypotheses using the D-statistic and a phylogenomic dataset of over 500 nuclear Anchored Hybrid Enrichment genes along with mitochondrial genomes. This larger dataset provided stronger support for some of our hybridization scenarios but not all. Using these same data we inferred phylogenetic networks using SNaQ and PhyNEST to determine whether the two methods recovered plausible network with respect to our hypothesized hybridization events. We found that both SNaQ and PhyNEST recovered an extensive history of reticulate evolution in New Zealand cicadas which broadly matched our predictions. We suggest that differences between networks inferred by the two network programs may result from using site patterns versus gene trees as input data or reflect other differences in the inference methods. Finally, we discuss considerations for users applying these methods to targeted enrichment data and suggest improvements for network method developers.
{"title":"Using Phylogenetic Network Methods for Genomic Data Exploration and Hypothesis Generation Fails to Untangle a Confusing History of Hybridization in New Zealand Cicadas.","authors":"Mark Stukel,Chris Simon","doi":"10.1093/sysbio/syag006","DOIUrl":"https://doi.org/10.1093/sysbio/syag006","url":null,"abstract":"Rapid species radiations make hybridization among species more likely. Detecting and reconstructing hybridization is therefore critical for understanding species relationships in many cases. We explored the relative performance of two phylogenetic network methods, SNaQ, a gene tree-based method, and PhyNEST, a site pattern-based method, in evaluating the plausibility of proposed past hybridization hypotheses. As our study system, we used the New Zealand cicada genera Kikihia and Maoricicada. Previous phylogenomic work on these two species radiations suggested multiple hybridization events in response to changing landscapes and climate. We generated hypotheses for specific hybridization events based on observed hybrid mating songs and patterns of mito-nuclear discordance from previous studies. We tested our hypotheses using the D-statistic and a phylogenomic dataset of over 500 nuclear Anchored Hybrid Enrichment genes along with mitochondrial genomes. This larger dataset provided stronger support for some of our hybridization scenarios but not all. Using these same data we inferred phylogenetic networks using SNaQ and PhyNEST to determine whether the two methods recovered plausible network with respect to our hypothesized hybridization events. We found that both SNaQ and PhyNEST recovered an extensive history of reticulate evolution in New Zealand cicadas which broadly matched our predictions. We suggest that differences between networks inferred by the two network programs may result from using site patterns versus gene trees as input data or reflect other differences in the inference methods. Finally, we discuss considerations for users applying these methods to targeted enrichment data and suggest improvements for network method developers.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"30 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146015322","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}
Lenoks, species within the genus Brachymystax, are freshwater salmonids with a scattered distribution in the rivers of Siberia, Northeast China, Xinjiang, Hebei, and the Qinling Mountains. Owing to long-term population declines, all species assigned to Brachymystax are protected by law in China. However, the evolutionary history and species-level systematics of this genus remain controversial, complicating taxonomic designations and conservation efforts. In particular, the geographical separation of populations may have resulted in the formation of phenotypically similar cryptic species. We built a chromosome-level genome assembly of B. tsinlingensis and re-sequenced the genomes of 103 individuals of Chinese Brachymystax spp. from five geographically isolated locations. Population genomic and phylogenomic analyses based on nuclear SNPs and mitochondrial genomes revealed six different genetic lineages of which at least one, the Hebei lineage, represents a cryptic species. Notably, the results suggest that the sympatric species B. lenok and B. tumensis are not close relatives, but the former is more closely related to the new species B. sp. Xinjiang with an estimated divergence time of c. 630 Ka, indicating that closely-related sympatric species may not have evolved via sympatric speciation in areas influenced by Pleistocene climate changes. We observed mito-nuclear phylogenomic discordance in Brachymystax caused by the strong gene flow between B. lenok and B. tumensis. Phylogenetic and demographic analyses emphasize the important role of interglacial refugia in promoting speciation and underscore the impact of historical gene flow. Compared to other lenoks, the Gansu population had the lowest genetic diversity, suggesting that particular attention to protect its genetic resources may be required. Finally, we suggest that cross-regional proliferation and release of lenoks should be banned in the future to protect the genetic integrity of these divergent groups.
{"title":"Population Genomics of Endangered Lenoks (Brachymystax spp.) in China Reveals the Presence of Cryptic Species.","authors":"Xinmiao Zhang,Judith E Mank,Sunandan Das,Chunlong Zhao,Peng Xie,Jilong Wang,Lixin Wang,Yu Jiang,Juha MerilÄ,Dongmei Xiong","doi":"10.1093/sysbio/syag004","DOIUrl":"https://doi.org/10.1093/sysbio/syag004","url":null,"abstract":"Lenoks, species within the genus Brachymystax, are freshwater salmonids with a scattered distribution in the rivers of Siberia, Northeast China, Xinjiang, Hebei, and the Qinling Mountains. Owing to long-term population declines, all species assigned to Brachymystax are protected by law in China. However, the evolutionary history and species-level systematics of this genus remain controversial, complicating taxonomic designations and conservation efforts. In particular, the geographical separation of populations may have resulted in the formation of phenotypically similar cryptic species. We built a chromosome-level genome assembly of B. tsinlingensis and re-sequenced the genomes of 103 individuals of Chinese Brachymystax spp. from five geographically isolated locations. Population genomic and phylogenomic analyses based on nuclear SNPs and mitochondrial genomes revealed six different genetic lineages of which at least one, the Hebei lineage, represents a cryptic species. Notably, the results suggest that the sympatric species B. lenok and B. tumensis are not close relatives, but the former is more closely related to the new species B. sp. Xinjiang with an estimated divergence time of c. 630 Ka, indicating that closely-related sympatric species may not have evolved via sympatric speciation in areas influenced by Pleistocene climate changes. We observed mito-nuclear phylogenomic discordance in Brachymystax caused by the strong gene flow between B. lenok and B. tumensis. Phylogenetic and demographic analyses emphasize the important role of interglacial refugia in promoting speciation and underscore the impact of historical gene flow. Compared to other lenoks, the Gansu population had the lowest genetic diversity, suggesting that particular attention to protect its genetic resources may be required. Finally, we suggest that cross-regional proliferation and release of lenoks should be banned in the future to protect the genetic integrity of these divergent groups.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"49 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005102","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}
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