Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1059 - 1065

Published: July 1, 2021

Language: Английский

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Species delimitation in the Polygonatum odoratum complex (Asparagaceae) based on phylogenomic and morphometric data

Taxon, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 28, 2025

Abstract Defining species and delineating boundaries among closely related is challenging particularly for complexes with a recent history of diversification. The Polygonatum odoratum complex, consisting seven taxa, presents compelling example showing unresolved taxonomic boundaries. Here, we aim to delimit in the complex using genomic morphometric data. Target enrichment was employed analyze 40 accessions representing taxa complex. We inferred tree coalescent maximum likelihood approaches nuclear plastid Additionally, examined 14 morphological characters from 851 herbarium specimens conducted analysis factor mixed phylogenomic analysis, based on 297 genes, strongly supports presence three monophyletic clades diversification (<4 million years). Coupled our examinations, findings demonstrate existence distinct species, revising previous classification taxa. By applying an integrated concept, study resolves updates taxonomy P.

Language: Английский

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Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 187, P. 107869 - 107869

Published: July 8, 2023

Language: Английский

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(3), P. 546 - 578

Published: Jan. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Language: Английский

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Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(3), P. 927 - 945

Published: Oct. 6, 2021

Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon-specific probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales within rapidly radiating clades. We present here newly developed target set Bromeliaceae, large ecologically diverse plant family with highly variable diversification rates. The targets 1776 coding regions, including genes putatively involved key innovations, the aim empower testing of wide range evolutionary hypotheses. compare relative this set, Bromeliad1776, Angiosperms353 kit. results higher enrichment success across entire family; however, overall performance both trees is relatively comparable, highlighting vast potential resolving relationships. For more detailed or genetic analyses, example exploration gene tree concordance, nucleotide diversity structure, presents clear benefits. discuss lessons that comparative study provides future investigations, particular radiations.La captura selectiva de secuencias ADN ha surgido como una herramienta importante para la filogenética y genética poblaciones en taxones no-modelo. Mientras que el desarrollo sondas específicas cada taxón requiere un esfuerzo sostenido, las colecciones universales disponibles pueden tener potencia disminuida reconstrucción relaciones filogenéticas poco profundas o radiaciones rápidas. Presentamos aquí conjunto desarrollado recientemente familia plantas extensa, ecológicamente diversa con tasas diversificación muy variables. El se centra regiones codificación, incluyendo supuestamente implicados rasgos innovación clave, objetivo potenciar comprobación amplia gama hipótesis evolutivas. Comparamos relativa este diseñado específico, colección Angiosperms353. específico da lugar mayor éxito toda familia. Sin embargo, rendimiento global ambos reconstruir árboles filogenéticos es relativamente lo pone manifiesto gran potencial los resolver Para análisis más detallados, por ejemplo exploración congruencia genes, diversidad nucleótidos estructura población, Bromeliaceae presenta claras ventajas. Discutimos lecciones potenciales estudio comparativo proporciona futuras investigaciones poblaciones,

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Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 195, P. 108064 - 108064

Published: March 19, 2024

The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, is distributed worldwide in temperate tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera ca. 160 species, restricted eastern Australia, New Zealand, Guinea. species show an impressive range growth habit, from small herbs ericoid subshrubs medium-sized trees. They live a wide habitats are often dominant subalpine alpine vegetation. Despite well-supported circumscription Celmisiinae, uncertainties have remained about their internal relationships classification at genus levels. This study exploited recent advances high-throughput sequencing build robust multi-gene phylogeny for subtribe Celmisiinae. target enrichment Angiosperms353 bait set hybpiper-nf paragone-nf pipelines were used retrieve, infer, assemble orthologous loci 75 taxa representing all main putative clades within subtribe. Because diploidised ploidy level as well missing data assemblies, uncertainty remains surrounding inference orthology detection. However, based on variety gene-family sets, coalescent concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy gene-families caused some problems, but estimated phylogenies well-resolved. phylogenomic evidence supported three clades: Pleurophyllum clade (Pleurophyllum, Macrolearia Damnamenia), mostly Zealand Subantarctic Islands, Celmisia mainland Shawia (including 'Olearia pro parte' Pachystegia) Australia results presented here add accumulating support efficient method documenting plant diversity.

Language: Английский

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Phylogenomics of Tetraopes longhorn beetles unravels their evolutionary history and biogeographic origins

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: March 27, 2024

Abstract Tetraopes longhorn beetles are known for their resistance to milkweed plant toxins and coevolutionary dynamics with plants ( Asclepias ). This association is considered a textbook example of coevolution, in which each species specialized feed on one or few . A major challenge investigating hypotheses conducting molecular ecology studies lies the limited understanding evolutionary history biogeographical patterns By integrating genomic, morphological, paleontological, geographical data, we present robust phylogeny relatives, using three inference methods varying subsets encompassing 2–12 thousand UCE loci. We elucidate diversification across regions colonization American continent. Our findings suggest that genus originated Central America approximately 21 million years ago during Miocene diversified from Mid-Miocene Pleistocene. These events coincided intense geological activity America. Additionally, independent North occurred Late early Pleistocene, potentially contributing group. data common ancestor Tetraopini migrated into America, likely facilitated by Atlantic land bridges, while closely related tribes diverged Asia Europe Paleocene. Establishing densely sampled provides foundation micro- macroevolutionary phenomena, including clinal variation, detoxification mechanisms this ecologically important

Language: Английский

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How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 12

Published: Jan. 7, 2022

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability incomplete lineage sorting (ILS), different topologies gene trees are expected, leading tree discordance, i.e., not all represent tree. Phylogenetic discordance common phylogenomic datasets, apart from ILS, additional sources include hybridization, whole-genome duplication, methodological artifacts. Despite a high degree often well supported further addressed studies, which can eventually lead incorrect phylogenetic hypotheses, especially We chose high-Andean Asteraceae genus Loricaria shed light on potential generated hypothesis. By accounting for paralogy during inference, we based hundreds nuclear loci, using Hyb-Seq, plastome phylogeny obtained off-target reads target enrichment. observed found implausible at first sight, because did show evidence hybridization previous studies. used various analyses (trees networks) as D-statistics test ILS developed into workflow how tackle recent radiations. strong within Loricaria. Low genetic differentiation was evident between located Andean cordilleras, could be indicative substantial introgression populations, promoted Pleistocene glaciations, when alpine habitats shifted creating opportunities secondary contact hybridization.

Language: Английский

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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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Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae)

PhytoKeys, Journal Year: 2025, Volume and Issue: 251, P. 87 - 118

Published: Jan. 16, 2025

Plant phylogenetics has been revolutionised in the genomic era, with target capture acting as primary workhorse of most recent research new field phylogenomics. Target (aka Hyb-Seq) allows researchers to sequence hundreds regions (loci) their choosing, at relatively low cost per sample, from which derive phylogenetically informative data. Although this highly flexible and widely applicable method rightly earned its place field's de facto standard, it does not come without challenges. In particular, users have specify loci sequence-a surprisingly difficult task, especially when working non-model groups, requires pre-existing resources form assembled genomes and/or transcriptomes. absence taxon-specific resources, sets exist that are designed work across broad taxonomic scales. However, conserved they may lack informativeness for phylogenetic problems, such presented by rapid radiation Erica southern Africa. We a set phylogenomics intended maximise minimise paralogy while maintaining universality including genes used Angiosperms353 set. Comprising just over 300 genes, targets had excellent recovery rates roughly 90 species well outgroups Calluna, Daboecia, Rhododendron, high information content measured parsimony sites Quartet Internode Resolution Probability (QIRP) shallow nodes. Notably, QIRP was positively correlated intron content, introns targets-rather than recovering them via exon-flanking "bycatch"-substantially improved recovery. Overall, our results show value building custom set, we provide suite open-source tools can be replicate approach other groups (https://github.com/SethMusker/TargetVet).

Language: Английский

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