Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 8, 2022

Subfamily Rubioideae is the largest of main lineages in coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes other major clades within this group plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from organellar genomes nuclear ribosomal DNA, we here use a large number low-copy genes obtained via target capture approach to infer phylogenetic Rubioideae. We included 101 representing all but two (the monogeneric Foonchewieae Aitchinsonieae) currently recognized tribes, one non-monogeneric tribe were represented by more than genus. Using 353 targeted universal Angiosperms353 probe set investigated impact type, analytical approach, potential paralogs on reconstruction. inferred robust hypothesis vast majority (or all) nodes being highly supported across analyses datasets few incongruences between topologies. The results similar those novel also identified. found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS levels support gene tree congruence. full (353 genes) potentially paralogous removed (186 increased incongruence slightly. pattern conflict at short internal branches often consistent high incomplete lineage sorting (ILS) due rapid speciation group. concatenation- coalescence-based trees agreed, observed discordance approaches may be best explained their differences accounting for ILS. greatly improved our confidence understanding phylogeny, highlighted previously uncertain possibility explore sources underlying discordance.

Language: Английский

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Estimating phylogenies from genomes: A beginners review of commonly used genomic data in vertebrate phylogenomics

Journal of Heredity, Journal Year: 2023, Volume and Issue: 114(1), P. 1 - 13

Published: Jan. 1, 2023

Abstract Despite the increasing feasibility of sequencing whole genomes from diverse taxa, a persistent problem in phylogenomics is selection appropriate genetic markers or loci for given taxonomic group research question. In this review, we aim to streamline decision-making process when selecting specific use phylogenomic studies by introducing commonly used types genomic markers, their evolutionary characteristics, and associated uses phylogenomics. Specifically, review utilities ultraconserved elements (including flanking regions), anchored hybrid enrichment loci, conserved nonexonic elements, untranslated regions, introns, exons, mitochondrial DNA, single nucleotide polymorphisms, anonymous regions (nonspecific that are evenly randomly distributed across genome). These various differ substitution rates, likelihood neutrality being strongly linked under selection, mode inheritance, each which important considerations reconstruction. features may give type marker advantages disadvantages depending on biological question, number taxa sampled, timescale, cost effectiveness, analytical methods used. We provide concise outline as resource efficiently consider key aspects marker. There many factors designing studies, serve primer weighing options between multiple potential markers.

Language: Английский

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Arthrological reconstructions of the pterosaur neck and their implications for the cervical position at rest

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e16884 - e16884

Published: Feb. 21, 2024

The lack of any pterosaur living descendants creates gaps in the knowledge biology this group, including its cervical biomechanics, which makes it difficult to understand their posture and life habits. To mitigate part issue, we reconstructed osteology arthrology three pterosaurs, allowing us make inferences about position neck these animals at rest. We used scans three-dimensionally preserved series Anhanguera piscator , Azhdarcho lancicollis Rhamphorhynchus muensteri for reconstructions, thus representing different lineages. For recognition ligaments, joint cartilages, levels overlapping zygapophyses, applied Extant Phylogenetic Bracket method, based on various extant birds Caiman latirostris . inferred that intervertebral joints were probably covered by a thin layer synovial cartilage whose thickness varied along neck, being thicker posterior region. Ignoring can affect reconstructions. According vertebral angulation, was slightly sinuous when rest position. Our analyses also indicate pterosaurs had segmented supra-segmented articular could confer stabilization, execute passive forces store elastic energy.

Language: Английский

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Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(5), P. e0302365 - e0302365

Published: May 20, 2024

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage off-target proportion reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly resulted comprehensive dataset robust inference phylogenetic relationships, where most intratribal intertribal are resolved with strong support. While results were mostly agreement studies data, novel plastid perspective also detected. For example, our analyses provide support for SCOUT clade its sister relationship remaining members subfamily, which differs from but agrees recent data. However, several instances highly supported discordance identified across phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain majority discordant introgression may be better explanation some cases. Our further plastomes are, few exceptions, conserved mainly conform structure, gene content, order present flowering plants.

Language: Английский

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Flesh and bone: The musculature and cervical movements of pterosaurs

Anais da Academia Brasileira de Ciências, Journal Year: 2025, Volume and Issue: 97(suppl 1)

Published: Jan. 1, 2025

The osteological variations present in the cervical vertebrae of pterosaurs represent changes soft tissues neck and reflect their function. Here, we infer presence, volume, capacity musculature pterosaurs. We performed our analyses on three-dimensionally preserved series Anhanguera sp. (AMNH 22555), piscator (NSM-PV 19892), Azhdarcho lancicollis (ZIN PH CCMGE, several specimens), Rhamphorhynchus muensteri (MGUH 1891.738), last three which were digitally modeled for muscle reconstruction. identified correlates from structures observed extant archosaur skulls supported by Extant Phylogenetic Bracket (EPB) criteria. estimated muscular using "Maximal Force Production" formula. According to analyses, at least thirteen muscles pterosaurs, only one does not correspond an EPB level I inference. that skull pitching more robust stronger execute movements. Muscles showed extremely low potential had a stabilization Specializations are compatible with foraging habits previously inferred these namely surface fishing capture small terrestrial prey Azhdarcho.

Language: Английский

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Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(19)

Published: May 2, 2025

Current genome sequencing initiatives across a wide range of life forms offer significant potential to enhance our understanding evolutionary relationships and support transformative biological medical applications. Species trees play central role in many these applications; however, despite the widespread availability assemblies, accurate inference species remains challenging due limited automation, substantial domain expertise, computational resources required by conventional methods. To address this limitation, we present ROADIES, fully automated pipeline infer starting from raw assemblies. In contrast prominent approach, ROADIES incorporates unique strategy randomly sampling segments input genomes generate gene trees. This eliminates need for predefining set loci, limiting analyses fixed number genes, performing cumbersome annotation and/or whole alignment steps. also orthology leveraging existing discordance-aware methods that allow multicopy genes. Using genomic datasets large-scale efforts four diverse (placental mammals, pomace flies, birds, budding yeasts), show infers are comparable quality state-of-the-art studies but fraction time effort, including on with rampant tree discordance complex polyploidy. With its speed, accuracy, has vastly simplify inference, making it accessible broader scientists

Language: Английский

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wQFM: highly accurate genome-scale species tree estimation from weighted quartets

Bioinformatics, Journal Year: 2021, Volume and Issue: 37(21), P. 3734 - 3743

Published: June 3, 2021

Abstract Motivation Species tree estimation from genes sampled throughout the whole genome is complicated due to gene tree–species discordance. Incomplete lineage sorting (ILS) one of most frequent causes for this discordance, where alleles can coexist in populations periods that may span several speciation events. Quartet-based summary methods estimating species trees a collection are becoming popular their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, weights correspond relative importance quartets, subsequently amalgamating weighted infer single coherent allow statistically consistent way trees. However, handling challenging. Results We propose wQFM, highly accurate method multi-locus data, by extending quartet FM (QFM) algorithm setting. wQFM was assessed on simulated real biological datasets, including avian phylogenomic dataset, which largest datasets date. compared wQMC, best alternate amalgamation, ASTRAL, widely used coalescent-based methods. Our results suggest matches or improves upon wQMC ASTRAL. Availability implementation Datasets studied article (in open-source form) available at https://github.com/Mahim1997/wQFM-2020. Supplementary information data Bioinformatics online.

Language: Английский

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Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 3, 2024

The evolutionary histories of different genomic regions typically differ from each other and the underlying species phylogeny. This makes tree estimation challenging. Here, we examine performance phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, living birds. We compared trees generated by maximum likelihood (ML) analysis concatenated data, gene summary methods, SVDquartets. also conduct first empirical test “new” method called METAL (Metric algorithm for Estimation Trees based on Aggregation Loci), which is distances calculated data. conducted this novel dataset comprising more than 4,000 ultraconserved element (UCE) loci almost all bird families two existing UCE intron datasets sampled avian orders. identified “reliable clades” very likely to be present in true used them assess performance. ML analyses data recovered reliable clades with less greater robustness missing methods. clades, but only performed well largest datasets. Gene (weighted ASTRAL weighted ASTRID) well; they required concatenation. SVDquartets exhibited worst tested. In addition methodological insights, study provides estimate 99% currently recognized families. Only one 181 examined was consistently resolved differently concatenation versus suggesting it may possible achieve consensus deep extant

Language: Английский

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FASTRAL: improving scalability of phylogenomic analysis

Bioinformatics, Journal Year: 2021, Volume and Issue: 37(16), P. 2317 - 2324

Published: Feb. 5, 2021

ASTRAL is the current leading method for species tree estimation from phylogenomic datasets (i.e. hundreds to thousands of genes) that addresses gene discord resulting incomplete lineage sorting (ILS). statistically consistent under multi-locus coalescent model (MSC), runs in polynomial time, and able run on large datasets. Key ASTRAL's algorithm use dynamic programming find an optimal solution MQSST (maximum quartet support supertree) within a constraint space it computes input. Yet, can fail complete reasonable timeframes with many genes species, because these cases too large.Here, we introduce FASTRAL, method. FASTRAL based ASTRAL, but uses different technique constructing space. The define maintains statistical consistency time; thus prove time MSC. Our performance study both biological simulated demonstrates matches or improves respect topology accuracy (and high ILS conditions significantly more accurate), while being dramatically faster-especially numbers ILS-due using smaller space.FASTRAL available open-source form at https://github.com/PayamDiba/FASTRAL.Supplementary data are Bioinformatics online.

Language: Английский

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Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction

Science Advances, Journal Year: 2024, Volume and Issue: 10(31)

Published: July 31, 2024

Complex patterns of genome evolution associated with the end-Cretaceous [Cretaceous-Paleogene (K-Pg)] mass extinction limit our understanding early evolutionary history modern birds. Here, we analyzed avian molecular and identified distinct macroevolutionary regimes across exons, introns, untranslated regions, mitochondrial genomes. Bird clades originating near K-Pg boundary exhibited numerous shifts in mode evolution, suggesting a burst genomic heterogeneity at this point Earth's history. These inferred substitution were closely related to developmental mode, adult body mass, metabolic scaling. Our results suggest that triggered integrated genomes, physiology, life dawn bird radiation.

Language: Английский

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