Systematic Biology最新文献

{"title":"Site-specific structure and stability constrained substitution models improve phylogenetic inference","authors":"Ivan Lorca-Alonso, Otero-de-Navascues Fernando, Miguel Arenas, Ugo Bastolla","doi":"10.1093/sysbio/syaf007","DOIUrl":"https://doi.org/10.1093/sysbio/syaf007","url":null,"abstract":"In previous studies, we presented our site-specific Stability Constrained substitution models of Protein Evolution (Stab-CPE) that define fitness as the probability of finding a protein folded in its native state but ignore changes in the native structure. Stab-CPE models can be used to predict a more realistic evolutionary variability across protein sites, nevertheless they still qualitatively differ from observed data and appear too tolerant to mutations. Here we present novel structurally constrained substitution models (Str-CPE) that define fitness based on the structural deformation produced by a mutation, which we predict adopting an extension of Juli’an Echaveás linearly forced elastic network model. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSAs) that include one or more known structures, and better predict the observed conservation across sites. The models that combine Str-CPE and Stab-CPE models are even more stringent and fit the empirical MSAs better. We collectively refer to our models as Structure and Stability Constrained substitution models of Protein Evolution (SSCPE). When using distantly-related proteins, we find that more similar phylogenies are inferred under the SSCPE models than under traditional empirical substitution models if compared to the corresponding reference phylogenies inferred using structural distances. Therefore, SSCPE models seem to be much better-fitting substitution models for deep phylogeny inference. The SSCPE models have been implemented in the PERL-based program SSCPE.pl, which uses RAxML-NG to infer phylogenies under the SSCPE model given a concatenated MSA and a list of protein structures that match the sequences in the MSA.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"5 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143866191","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":"PlaceMyFossils: An Integrative Approach to Analyze and Visualize the Phylogenetic Placement of Fossils Using Backbone Trees.","authors":"Santiago A Catalano,Ignacio Escapa,Kelsey D Pugh,Ashley S Hammond,Pablo Goloboff,Sergio Almécija","doi":"10.1093/sysbio/syaf025","DOIUrl":"https://doi.org/10.1093/sysbio/syaf025","url":null,"abstract":"In recent years, there has been a growing interest in using morphology to establish the placement of species on phylogenetic trees derived from molecular data. This is relevant in the case of recently extinct or fossil species, which are usually represented only by fragmentary morphology. In the latter case, constrained analyses using backbone trees have also proven helpful in evaluating the placement of fragmentary specimens on phylogenetic trees derived from morphological data. Consequently, several available phylogenetic programs now include functions to run constrained searches. However, a comprehensive evaluation of the obtained results is not readily available within existing analytical tools. Here, we present an integrated approach-PlaceMyFossils-specifically designed to (1) thoroughly evaluate the phylogenetic placement of given query species (especially fossils) on a reference tree, (2) determine which characters and character partitions are most relevant in defining the phylogenetic placement, (3) assess the confidence of the results, and (4) define the optimal analytical conditions to place the query species. PlaceMyFossils combines several analyses implemented as an interactive script for TNT (Tree Analysis Using New Technologies software), a popular-and free-phylogenetic software that is widely used in paleontological studies. Finally, we demonstrate the utility and investigate the performance of PlaceMyFossils compared to other available tools using two disparate empirical datasets drawn from conifers and dinosaurs. While primarily designed for working with fossils, this tool also holds great potential for advancing morphological and molecular systematics. It offers a powerful resource for empirical systematists aiming to integrate molecular and morphological data. This is particularly relevant given the growing interest in morphological evolution as a complementary perspective on evolutionary processes and the drivers of diversification.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"122 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143846434","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":"Evolution of Large Eyes in Stromboidea (Gastropoda): Impact of Photic Environment and Life History Traits.","authors":"Alison R Irwin, Nicholas W Roberts, Ellen E Strong, Yasunori Kano, Daniel I Speiser, Elizabeth M Harper, Suzanne T Williams","doi":"10.1093/sysbio/syae063","DOIUrl":"10.1093/sysbio/syae063","url":null,"abstract":"<p><p>Eyes within the marine gastropod superfamily Stromboidea range widely in size, from 0.2 to 2.3 mm-the largest eyes known in any gastropod. Despite this interesting variation, the underlying evolutionary pressures remain unknown. Here, we use the wealth of material available in museum collections to explore the evolution of stromboid eye size and structure. Our results suggest that depth is a key light-limiting factor in stromboid eye evolution; here, increasing water depth is correlated with increasing aperture width relative to lens diameter, and therefore an increasing investment in sensitivity in dim light environments. In the major clade containing all large-eyed stromboid families, species observed active during the day and the night had wider eye apertures relative to lens sizes than species observed active during the day only, thereby prioritizing sensitivity over resolution. Species with no consistent diel activity pattern also had smaller body sizes than exclusively day-active species, which may suggest that smaller animals are more vulnerable to shell-crushing predators, and avoid the higher predation pressure experienced by animals active during the day. Within the same major clade, ancestral state reconstruction suggests that absolute eye size increased above 1 mm twice. The unresolved position of Varicospira, however, weakens this hypothesis and further work with additional markers is needed to confirm this result.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"301-322"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584383","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":"Exploring the Macroevolutionary Signature of Asymmetric Inheritance at Speciation.","authors":"Théo Gaboriau, Joseph A Tobias, Daniele Silvestro, Nicolas Salamin","doi":"10.1093/sysbio/syae043","DOIUrl":"10.1093/sysbio/syae043","url":null,"abstract":"<p><p>Popular comparative phylogenetic models such as Brownian Motion, Ornstein-Ulhenbeck, and their extensions assume that, at speciation, a trait value is inherited identically by 2 descendant species. This assumption contrasts with models of speciation at a micro-evolutionary scale where descendants' phenotypic distributions are sub-samples of the ancestral distribution. Different speciation mechanisms can lead to a displacement of the ancestral phenotypic mean among descendants and an asymmetric inheritance of the ancestral phenotypic variance. In contrast, even macro-evolutionary models that account for intraspecific variance assume symmetrically conserved inheritance of ancestral phenotypic distribution at speciation. Here, we develop an Asymmetric Brownian Motion model (ABM) that relaxes the assumption of symmetric and conserved inheritance of the ancestral distribution at the time of speciation. The ABM jointly models the evolution of both intra- and inter-specific phenotypic variation. It also infers the mode of phenotypic inheritance at speciation, which can range from a symmetric and conserved inheritance, where descendants inherit the ancestral distribution, to an asymmetric and displaced inheritance, where descendants inherit divergent phenotypic means and variances. To demonstrate this model, we analyze the evolution of beak morphology in Darwin finches, finding evidence of displacement at speciation. The ABM model helps to bridge micro- and macro-evolutionary models of trait evolution by providing a more robust framework for testing the effects of ecological speciation, character displacement, and niche partitioning on trait evolution at the macro-evolutionary scale.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"267-281"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141752781","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}

{"title":"Biogeographic History of Pigeons and Doves Drives the Origin and Diversification of Their Parasitic Body Lice.","authors":"Andrew D Sweet, Jorge Doña, Kevin P Johnson","doi":"10.1093/sysbio/syae038","DOIUrl":"10.1093/sysbio/syae038","url":null,"abstract":"<p><p>Despite their extensive diversity and ecological importance, the history of diversification for most groups of parasitic organisms remains relatively understudied. Elucidating broad macroevolutionary patterns of parasites is challenging, often limited by the availability of samples, genetic resources, and knowledge about ecological relationships with their hosts. In this study, we explore the macroevolutionary history of parasites by focusing on parasitic body lice from doves. Building on extensive knowledge of ecological relationships and previous phylogenomic studies of their avian hosts, we tested specific questions about the evolutionary origins of the body lice of doves, leveraging whole genome data sets for phylogenomics. Specifically, we sequenced whole genomes from 68 samples of dove body lice, including representatives of all body louse genera from 51 host taxa. From these data, we assembled > 2300 nuclear genes to estimate dated phylogenetic relationships among body lice and several outgroup taxa. The resulting phylogeny of body lice was well supported, although some branches had conflicting signals across the genome. We then reconstructed ancestral biogeographic ranges of body lice and compared the body louse phylogeny to the phylogeny of doves, and also to a previously published phylogeny of the wing lice of doves. Divergence estimates placed the origin of body lice in the late Oligocene. Body lice likely originated in Australasia and dispersed with their hosts during the early Miocene, with subsequent codivergence and host switching throughout the world. Notably, this evolutionary history is very similar to that of dove wing lice, despite the stronger dispersal capabilities of wing lice compared to body lice. Our results highlight the central role of the biogeographic history of host organisms in driving the evolutionary history of their parasites across time and geographic space.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"198-214"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141734980","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":"Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield.","authors":"Mathilde Barthe, Loïs Rancilhac, Maria C Arteaga, Anderson Feijó, Marie-Ka Tilak, Fabienne Justy, William J Loughry, Colleen M McDonough, Benoit de Thoisy, François Catzeflis, Guillaume Billet, Lionel Hautier, Nabholz Benoit, Frédéric Delsuc","doi":"10.1093/sysbio/syae027","DOIUrl":"10.1093/sysbio/syae027","url":null,"abstract":"<p><p>The nine-banded armadillo (Dasypus novemcinctus) is the most widespread xenarthran species across the Americas. Recent studies have suggested it is composed of 4 morphologically and genetically distinct lineages of uncertain taxonomic status. To address this issue, we used a museomic approach to sequence 80 complete mitogenomes and capture 997 nuclear loci for 71 Dasypus individuals sampled across the entire distribution. We carefully cleaned up potential genotyping errors and cross-contaminations that could blur species boundaries by mimicking gene flow. Our results unambiguously support 4 distinct lineages within the D. novemcinctus complex. We found cases of mito-nuclear phylogenetic discordance but only limited contemporary gene flow confined to the margins of the lineage distributions. All available evidence including the restricted gene flow, phylogenetic reconstructions based on both mitogenomes and nuclear loci, and phylogenetic delimitation methods consistently supported the 4 lineages within D. novemcinctus as 4 distinct species. Comparable genetic differentiation values to other recognized Dasypus species further reinforced their status as valid species. Considering congruent morphological results from previous studies, we provide an integrative taxonomic view to recognize 4 species within the D. novemcinctus complex: D. novemcinctus, D. fenestratus, D. mexicanus, and D. guianensis sp. nov., a new species endemic of the Guiana Shield that we describe here. The 2 available individuals of D. mazzai and D. sabanicola were consistently nested within D. novemcinctus lineage and their status remains to be assessed. The present work offers a case study illustrating the power of museomics to reveal cryptic species diversity within a widely distributed and emblematic species of mammals.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"177-197"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141440907","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}

{"title":"Exploring Phylogenetic Signal in Multivariate Phenotypes by Maximizing Blomberg's K.","authors":"Philipp Mitteroecker, Michael L Collyer, Dean C Adams","doi":"10.1093/sysbio/syae035","DOIUrl":"10.1093/sysbio/syae035","url":null,"abstract":"<p><p>Due to the hierarchical structure of the tree of life, closely related species often resemble each other more than distantly related species; a pattern termed phylogenetic signal. Numerous univariate statistics have been proposed as measures of phylogenetic signal for single phenotypic traits, but the study of phylogenetic signal for multivariate data, as is common in modern biology, remains challenging. Here, we introduce a new method to explore phylogenetic signal in multivariate phenotypes. Our approach decomposes the data into linear combinations with maximal (or minimal) phylogenetic signal, as measured by Blomberg's K. The loading vectors of these phylogenetic components or K-components can be biologically interpreted, and scatterplots of the scores can be used as a low-dimensional ordination of the data that maximally (or minimally) preserves phylogenetic signal. We present algebraic and statistical properties, along with 2 new summary statistics, KA and KG, of phylogenetic signal in multivariate data. Simulation studies showed that KA and KG have higher statistical power than the previously suggested statistic Km⁢u⁢l⁢t, especially if phylogenetic signal is low or concentrated in a few trait dimensions. In 2 empirical applications to vertebrate cranial shape (crocodyliforms and papionins), we found statistically significant phylogenetic signal concentrated in a few trait dimensions. The finding that phylogenetic signal can be highly variable across the dimensions of multivariate phenotypes has important implications for current maximum likelihood approaches to phylogenetic signal in multivariate data.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"215-229"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545292","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}

{"title":"Bayesian Selection of Relaxed-Clock Models: Distinguishing between Independent and Autocorrelated Rates.","authors":"Muthukumaran Panchaksaram, Lucas Freitas, Mario Dos Reis","doi":"10.1093/sysbio/syae066","DOIUrl":"10.1093/sysbio/syae066","url":null,"abstract":"<p><p>In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for branches in the phylogeny, with independent and autocorrelated rate models being commonly used. The two classes of models, however, can result in markedly different divergence time estimates for the same data set, and thus selecting the best rate model appears important for obtaining reliable inferences of divergence times. However, the properties of Bayesian rate model selection are not well understood, in particular when the number of sequence partitions analyzed increases and when age calibrations (such as fossil calibrations) are misspecified. Furthermore, Bayesian rate model selection is computationally expensive as it requires the calculation of marginal likelihoods by Markov Chain Monte Carlo sampling, and therefore, methods that can speed up the model selection procedure without compromising its accuracy are desirable. In this study, we use a combination of computer simulations and real data analysis to investigate the statistical behavior of Bayesian rate model selection and we also explore approximations of the likelihood to improve computational efficiency in large phylogenomic data sets. Our simulations demonstrate that the posterior probability for the correct rate model converges to one as more molecular sequence partitions are analyzed and when no calibrations are used, as expected due to asymptotic Bayesian model selection theory. Furthermore, we also show the model selection procedure is robust to slight misspecification of calibrations, and reliable inference of the correct rate model is possible in this case. However, we show that when calibrations are seriously misspecified, calculated model probabilities are completely wrong and may converge to one for the wrong rate model. Finally, we demonstrate that approximating the phylogenetic likelihood under an arcsine branch-length transform can dramatically reduce the computational cost of rate model selection without compromising accuracy. We test the approximate procedure on two large phylogenies of primates (372 species) and flowering plants (644 species), replicating results obtained on smaller data sets using exact likelihood. Our findings and methodology can assist users in selecting the optimal rate model for estimating times and rates along the Tree of Life.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"323-334"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142682823","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":"Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia.","authors":"Bernat Burriel-Carranza, Héctor Tejero-Cicuéndez, Albert Carné, Gabriel Mochales-Riaño, Adrián Talavera, Saleh Al Saadi, Johannes Els, Jiří Šmíd, Karin Tamar, Pedro Tarroso, Salvador Carranza","doi":"10.1093/sysbio/syae032","DOIUrl":"10.1093/sysbio/syae032","url":null,"abstract":"<p><p>Advances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These span from broad biogeographic patterns to population dynamics and adaptations to these environments. However, significant challenges remain in integrating large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, especially in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. In the present study, we assembled a de novo genome-wide SNP dataset for the complete endemic reptile fauna of a mountain range (19 described species with more than 600 specimens sequenced), and integrated state-of-the-art biogeographic analyses at the population, species, and community level. Thus, we provide a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain system. Our results show that reptiles independently colonized the Hajar Mountains of southeastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 deep lineages. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Interestingly, orogenic events do not seem key drivers of the biogeographic history of reptiles in this system. Instead, past climatic events seem to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid and semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Overall, our study does not only provide a valuable contribution to understanding the evolution of mountain biodiversity, but also offers a flexible and scalable approach that can be reproduced into any taxonomic group and at any discrete environment.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":"230-249"},"PeriodicalIF":6.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141493496","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}

{"title":"Phylogenomics resolve the systematics and biogeography of the ant tribe Myrmicini and tribal relationships within the hyperdiverse ant subfamily Myrmicinae","authors":"Matthew Prebus, Christian Rabeling","doi":"10.1093/sysbio/syaf022","DOIUrl":"https://doi.org/10.1093/sysbio/syaf022","url":null,"abstract":"Ants are a globally distributed and highly diverse group of eusocial animals, playing key ecological roles in most of the world’s terrestrial ecosystems. Our understanding of the processes involved in the evolution of this diverse family is contingent upon our knowledge of the phylogeny of the ants. While relationships among most subfamilies have come into resolution recently, several of the tribal relationships within the hyperdiverse subfamily Myrmicinae persistently conflict between or within studies, mirroring the controversial relationships of the Leptanillinae and Martialinae to the remaining ant subfamilies. Another persistent issue of debate in ant phylogenetics is the timing of major evolutionary events as inferred via divergence dating. Here, we test the topology of the myrmicine tribes using genome scale data, inspect gene tree-species tree concordance, and use posterior predictive checks and tests of compositional heterogeneity to infer sequence characteristics which potentially introduce systematic bias in myrmicine tribal topology. Furthermore, we test the placement of the Baltic amber fossil †Manica andrannae by integrating phylogenomic and morphological data from nearly all species within the genus Manica, and a broad sampling of its sister genus Myrmica. Subsequently, we demonstrate the effect of fossil placement on overall divergence times in the Myrmicinae. We then re-evaluate the historical biogeography of the Myrmicini and Pogonomyrmecini considering newly generated genetic data and insights from our phylogenomic results. We find that our current understanding of tribal topology in the Myrmicinae is strongly supported, but this topology is highly sensitive to compositional heterogeneity and gene-tree species-tree conflict. Our fossil placement analyses strongly suggest that †Manica andrannae is a stem Manica species, and analysis of this fossil in context of the Myrmicinae demonstrates that a single fossil calibration point can have broad-scale cascading effects on divergence dates within the entire subfamily. The results of our biogeographic reconstructions indicate a South American origin for the Pogonomyrmecini + Myrmicini. Additionally, our results suggest that the MRCA of Myrmica may have inhabited the western Nearctic in the early Miocene prior to repeated dispersal across Beringia throughout the Miocene and Pliocene. The MRCA of Manica, on the other hand, was inferred to have a Holarctic range prior to vicariance during the Pliocene. Unexpectedly, we found strong support in the Pogonomyrmecini for three coordinated dispersal events from South to Central America during the early Miocene, which has been previously proposed as an early biotic interchange event prior to the more commonly accepted 3.5 Ma closure of the Isthmus of Panama.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"183 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736827","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}