Systematic Biology最新文献

{"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":"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":"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":"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":"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}

{"title":"Massive inter-species introgression overwhelms phylogenomic relationships among jaguar, lion, and leopard.","authors":"Sarah H D Santos, Henrique V Figueiró, Tomas Flouri, Emiliano Ramalho, Laury Cullen, Ziheng Yang, William J Murphy, Eduardo Eizirik","doi":"10.1093/sysbio/syaf021","DOIUrl":"https://doi.org/10.1093/sysbio/syaf021","url":null,"abstract":"<p><p>Phylogenomic analyses of closely related species allow important glimpses into their evolutionary history. Although recent studies have demonstrated that interspecies hybridization has occurred in several groups, incorporating this process in phylogenetic reconstruction remains challenging. Specifically, the most predominant topology across the genome is often assumed to reflect the speciation tree, but rampant hybridization might overwhelm the genomes, causing that assumption to be violoated. The notoriously challenging phylogeny of the five extant Panthera species (specifically jaguar [P. onca], lion [P. leo], and leopard [P. pardus]) is an interesting system to address this problem. Here we employed a Panthera-wide whole-genome-sequence dataset incorporating three jaguar genomes and two representatives of lions and leopards to dissect the relationships among these three species. Maximum-likelihood trees reconstructed from non-overlapping genomic fragments of four different sizes strongly supported the monophyly of all three species. The most frequent topology (76-95%) united lion+leopard as sister-species (topology 1), followed by lion+jaguar (topology 2: 4-8%) and leopard+jaguar (topology 3: 0-6%). Topology 1 was dominant across the genome, especially in high-recombination regions. Topologies 2 and 3 were enriched in low-recombination segments, likely reflecting the species tree in the face of hybridization. Divergence times between sister-species of each topology, corrected for local recombination rate effects, indicated that the lion-leopard divergence was significantly younger than the alternatives, likely driven by post-speciation admixture. Introgression analyses detected pervasive hybridization between lions and leopards, regardless of the assumed species tree. This inference was strongly supported by multi-species-coalescence-with-introgression (MSci) analyses, which rejected topology 1 or any model without introgression. Interestingly, topologies 2 and 3 with extensive lion-leopard introgression were unidentifiable, highlighting the complexity of this phylogenetic problem. Our results suggest that the dominant genome-wide tree topology is not the true species tree but rather a consequence of overwhelming post-speciation admixture between lion and leopard.</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701546","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 Diversity Patterns are Explained by Diversification Rates and Dispersal at Ancient, not Shallow, Timescales.","authors":"Patrick R Stephens, Maxwell J Farrell, T Jonathan Davies, John L Gittleman, Shai Meiri, Matthew O Moreira, Uri Roll, John J Wiens","doi":"10.1093/sysbio/syaf018","DOIUrl":"https://doi.org/10.1093/sysbio/syaf018","url":null,"abstract":"<p><p>Explaining global species richness patterns is a major goal of evolution, ecology, and biogeography. These richness patterns are often attributed to spatial variation in diversification rates (speciation minus extinction). Surprisingly, prominent studies of birds, fish, and plants have reported higher speciation and/or diversification rates at higher latitudes, where species richness is lower. We hypothesize that these surprising findings are explained by the focus of those studies on relatively recent macroevolutionary rates, within the last ~20 million years. Here, we analyze global richness patterns among 10,213 squamates (lizards and snakes) and explore their underlying causes. We find that when diversification rates were quantified at more recent timescales, we observed mismatched patterns of rates and richness, similar to previous studies in other taxa. Importantly, diversification rates estimated over longer timescales were instead positively related to geographic richness patterns. These observations may help resolve the paradoxical results of previous studies in other taxa. We found that diversification rates were largely unrelated to climate, even though climate and richness were related. Instead, higher tropical richness was related to ancient occupation of tropical regions, with colonization time the variable that explained the most variation in richness overall. We suggest that large-scale diversity patterns might be best understood by considering climate, deep-time diversification rates, and the time spent in different regions, rather than recent diversification rates alone. [Climate, colonization time, diversification rate, lizards, latitudinal diversity gradient, snakes, species richness].</p>","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":" ","pages":""},"PeriodicalIF":6.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Aquatic biotas of Sundaland are fragmented but not refugial","authors":"Erwan Delrieu-Trottin, Selim Ben Chehida, Tedjo Sukmono, Hadi Dahruddin, Arni Sholihah, Kustiati Kustiati, Yuli Fitriana, Zainal Abidin Muchlisin, Roza Elvyra, Arif Wibowo, Ilham Vemandra Utama, Ujang Nurhaman, Sopian Sauri, Renny Risdawati, Muhamad Syamsul Arifin Zein, Juliette Pouzadoux, Jean-François Agnèse, Marie-Ka Tilak, Lawrence M Page, Thomas von Rintelen, Daisy Wowor, Dirk Steinke, Stefano Mona, Lukas Rüber, Paul D N Hebert, Nicolas Hubert","doi":"10.1093/sysbio/syaf005","DOIUrl":"https://doi.org/10.1093/sysbio/syaf005","url":null,"abstract":"Tropical insular systems have long attracted biologists, stimulating some important controversies in ecology and evolution. Eustatic fluctuations during the Pleistocene have been invoked to explain species dispersal and proliferation in these fragmented systems by controlling the extent of landmasses and their temporary connections. In ancient archipelagos, the Pleistocene represents only a small slice of their history so long-standing configurations might better explain insular diversity patterns. With a geological history of ca. 30 million years, the Sunda Shelf is old. Upon entering the Pleistocene, islands of the Sunda Shelf repeatedly separated and merged; however, recent reappraisals of its paleoenvironments and evolutionary dynamics have questioned their biogeographic significance. Based on the molecular inventory of six common freshwater fish families, we explored population fragmentation and demographic history of the most common species using mitochondrial DNA sequences. Species delimitation methods, applied to 1,062 sequences belonging to 37 species from 188 sites, detected 95 Molecular Operational Taxonomic Units (MOTUs). Among the nine most widespread species, the number of MOTUs ranged from 1 to 11, and correlated with time to the most recent common ancestor. Extended Bayesian Skyline Plots applied to mitogenomes and cytochrome c oxidase I sequences detected no variation in past effective population size within MOTUs, while hierarchical Approximate Bayesian Computation provided no evidence of congruent changes in effective population sizes. Fragmentation of an ancestral range is the most likely explanation for the rampant cryptic diversity observed, but demographic inferences do not support MOTUs as being refugial from an evolutionary perspective.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"43 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomics of marine angelfishes: diagnosing sources of systematic discordance for an iconic reef fish family (F: Pomacanthidae)","authors":"Lauriane M Baraf, Julia Y Hung, Peter F Cowman","doi":"10.1093/sysbio/syaf016","DOIUrl":"https://doi.org/10.1093/sysbio/syaf016","url":null,"abstract":"Genome-scale datasets are resolving challenging nodes across the tree of life. These datasets however, characterized by inherent heterogeneity, often push traditional phylogenetic reconstruction methods to their limits. By integrating multiple phylogenomic approaches, we can identify the causes of topological discordance within genomic partitions while accounting for various sources of heterogeneity and systematic errors. Here we conduct the first in-depth analysis of discordance for the reef family Pomacanthidae (marine angelfishes) using target enrichment data of ~1,000 ultraconserved elements from 45 pomacanthid species. Our combined phylogenomic approach resolved the systematics of the family at the base of the pomacanthid tree. Despite this resolution, our analyses also highlight discordance in ancestral nodes associated with the paraphyletic Centropyge genus and monotypic Pygoplites lineage, and the impact of incomplete lineage sorting in the evolutionary history pomacanthids. Species network searches and model selection supported a reticulated evolutionary history suggesting three ancient gene flow events between ghost (or unsampled) lineages at the root of the Pomacanthidae tree and ancestors of Genicanthus, Centropyge, Chaetodontoplus and Pomacanthus lineages. This study advances our understanding of diagnosing topological discordance in genome-scale phylogenies and provide an analytical pathway for limiting systematic errors. In the process of diagnosing discordance, we identify key evolutionary processes involved in the complex evolution of marine angelfishes. While often inconvenient in phylogenetic analyses, patterns of discordance can shed light on underlying biological and evolutionary processes that shape the evolution of biodiversity.","PeriodicalId":22120,"journal":{"name":"Systematic Biology","volume":"30 1","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}