A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(2), P. 301 - 319

Published: May 11, 2021

The tree of life is the fundamental biological roadmap for navigating evolution and properties on Earth, yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding evolutionary relationships. Here, we describe a comprehensive phylogenomic platform exploring angiosperm life, comprising set open tools based 353 nuclear genes targeted by universal Angiosperms353 sequence capture probes. primary goals this article (i) document methods, (ii) first release, (iii) present novel portal, Kew Tree Life Explorer (https://treeoflife.kew.org). We aim generate target all genera flowering plants, exploiting natural history collections such as herbarium specimens, augment it mined public data. Our described here, most extensive date, 3099 samples validated DNA barcode phylogenetic tests, representing 64 orders, 404 families (96$\%$) 2333 (17$\%$). A "first pass" was inferred from data, which totaled 824,878 sequences, 489,086,049 base pairs, 532,260 alignment columns, interactive presentation Explorer. This species generated using methods that were rigorous, tractable at scale operation. Despite limitations pertaining taxon gene sampling, recovery, models paralogy, strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders placing many time. set, intermediates openly accessible via will be updated further become available. major milestone toward complete plant opens doors highly integrated future phylogenomics through systematic standardized markers. approach has potential serve much-needed bridge between growing movement genomes Earth vast world's collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; phylogenomics; access; capture; life.].

Language: Английский

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Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genusLachemilla(Rosaceae)

New Phytologist, Journal Year: 2018, Volume and Issue: 218(4), P. 1668 - 1684

Published: March 31, 2018

Summary Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for reconstruction. Here, we use sequence capture data multiple species tree network approaches to resolve the backbone phylogeny of Neotropical genus Lachemilla , while distinguishing among sources incongruence. We used 396 nuclear loci nearly complete plastome sequences from 27 clarify relationships major groups explored conflict between gene trees inferred with plurality approaches. All methods recovered four previously proposed but different topologies these clades. Species analyses revealed that one clade, Orbiculate, is likely ancient hybrid origin, main trees. Additionally, found evidence potential whole genome duplication event shared by allied genera. shows clear recent hybridization throughout evolutionary history group. Also, show necessity can simultaneously accommodate sorting flow when studying patterns reticulation.

Language: Английский

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Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity

New Phytologist, Journal Year: 2019, Volume and Issue: 222(3), P. 1638 - 1651

Published: Feb. 8, 2019

The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, relationships among major lineages in remain unresolved, hampering comparative research. Here, we inferred a phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well sequenced genome 16 together 50 52 currently recognized tribes. A third samples were derived from herbarium material, facilitating broad taxonomic coverage family. Six clades formed successive sister groups to rest Brassicaceae. We also recovered strong support for novel tribes, resolved position taxa previously not assigned tribe. utility these phylogenetic results is illustrated through investigation genome-wide expression signatures that distinguish simple complex leaves Our study provides an easily extendable dataset further advances systematics timely higher-level framework wide range studies multiple traits intensively investigated group plants.

Language: Английский

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The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(3), P. 491 - 507

Published: Nov. 1, 2020

Abstract The genomic revolution offers renewed hope of resolving rapid radiations in the Tree Life. development multispecies coalescent model and improved gene tree estimation methods can better accommodate heterogeneity caused by incomplete lineage sorting (ILS) error stemming from short internal branches. However, relative influence these factors species inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci 64 taxa representing 39 families to infer flowering plant order Malpighiales. This includes 9 top 10 most unstable nodes angiosperms, which have been hypothesized arise radiation during Cretaceous. Here, show that coalescent-based do resolve backbone Malpighiales concatenation yield inconsistent estimations, providing evidence high this clade. Despite levels ILS error, our simulations demonstrate two alone are insufficient explain lack resolution order. To explore further, examined triplet frequencies among empirical trees discovered some them deviated significantly those attributed suggesting flow as an additional previously unappreciated phenomenon promoting variation Finally, applied novel method quantify contribution three primary sources demonstrated ILS, contributed 10.0$\%$, 34.8$\%$, 21.4$\%$ variation, respectively. Together, results suggest perfect storm likely resolution, further indicate recalcitrant phylogenetic relationships like may be represented networks. Thus, reducing such groups solely existing models adhere strictly bifurcating greatly oversimplifies reality, obscures ability more clearly discern process evolution. [Coalescent; concatenation; flanking region; introgression; phylogenomics; radiation, frequency.]

Language: Английский

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Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

American Journal of Botany, Journal Year: 2019, Volume and Issue: 106(4), P. 573 - 597

Published: April 1, 2019

Premise of the Study A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species‐rich. To extend understanding how shifts area, biomes, and pollinators impact diversification plants, we examined relationships these to across mega‐genus Salvia . Methods chronogram was developed from a supermatrix anchored hybrid enrichment genomic data targeted sequence for over 500 nearly 1000 species. Ancestral areas biomes were reconstructed using BioGeo BEARS Pollinator guilds scored, ancestral determined, pollinator identified, rates switches compared. Key Results well‐resolved phylogenetic backbone updated subgeneric designations presented. originated Southwest Asia Oligocene subsequently dispersed worldwide. Biome frequent likely lineage utilizing broadleaf and/or coniferous forests arid shrublands. None four species correlated biomes. Shifts pollination system not shifts, except one hummingbird shift that precedes major near crown New World subgen. Calosphace Multiple reversals back bee occurred within this clade. Conclusions diversified extensively different continents, with both bird pollinators. The lack tight correlation biome, most documented points other important drivers speciation

Language: Английский

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Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

Applications in Plant Sciences, Journal Year: 2020, Volume and Issue: 8(4)

Published: April 1, 2020

The reduced cost of high‐throughput sequencing and the development gene sets with wide phylogenetic applicability has led to rise sequence capture methods as a plausible platform for both phylogenomics population genomics in plants. An important consideration large targeted projects is per‐sample cost, which can be inflated when using off‐the‐shelf kits or reagents not purchased bulk. Here, we discuss reduce costs projects. We review minimal equipment consumable requirements while comparing several alternatives bulk DNA extraction, library preparation, target enrichment, sequencing. consider how each workflow alterations may affected by quality (e.g., fresh vs. herbarium tissue), genome size, scale project. provide calculator researchers considering use designing projects, identify challenges future low‐cost non‐model plant systems.

Language: Английский

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Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant GenusPolemonium(Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(1), P. 162 - 180

Published: June 24, 2020

Phylogenomic data from a rapidly increasing number of studies provide new evidence for resolving relationships in recently radiated clades, but they also pose challenges inferring evolutionary histories. Most existing methods reconstructing phylogenetic hypotheses rely solely on algorithms that only consider incomplete lineage sorting (ILS) as cause intra- or intergenomic discordance. Here, we utilize variety methods, including those to infer networks, account both ILS and introgression nuclear cytoplasmic-nuclear discordance using phylogenomic the flowering plant genus Polemonium (Polemoniaceae), an ecologically diverse Western North America with known suspected gene flow between species. We find widespread among loci can be explained by reticulate evolution history Polemonium. Furthermore, histories organellar genomes show strong inferred species tree genome. Discordance plastid genome is not completely ILS, one case detected events. Our results suggest multiple processes have been involved does accurately reflect relationships. discuss several potential causes this discordance, which emerging suggests more across Tree Life than previously thought. [Cyto-nuclear genomic capture, Polemoniaceae, Polemonium, reticulations.].

Language: Английский

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Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

New Phytologist, Journal Year: 2019, Volume and Issue: 226(4), P. 1158 - 1170

Published: April 9, 2019

Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from combination of vertical horizontal transmission may confound phylogenetic inference obscure our ability to accurately infer deep evolutionary history oaks. Using anchored enrichment, we obtained phylogenomic dataset consisting hundreds single-copy nuclear loci. Concatenation, species-tree network analyses were carried out in an attempt uncover signal ancient introgression divergent topology for oak clade. Locus site-level likelihood comparisons then conducted further explore introgressed dataset. Historical, intersectional is suggested occurred between ancestor Eurasian Roburoid lineage Quercus pontica North American Dumosae Prinoideae lineages. Despite extensive time past, approach proved successful detecting signature introgression. Our results, highlight importance sampling use plurality analytical tools methods sufficiently datasets, this signal, history.

Language: Английский

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Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 157, P. 107068 - 107068

Published: Jan. 9, 2021

Gesneriaceae (ca. 3400 species) is a pantropical plant family with wide range of growth form and floral morphology that are associated repeated adaptations to different environments pollinators. Although systematics has been largely improved by the use Sanger sequencing data, our understanding evolutionary history group still far from complete due limited number informative characters provided this type data. To overcome limitation, we developed here Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes Universal Angiosperms-353 kit. With an average 557,600 reads 87.8% recovery, target was successful across also other families Lamiales. From bait set, selected most 418 resolve phylogenetic relationships entire using maximum likelihood coalescent-based methods. Upon testing performance baits on 78 taxa representing 20 out 24 subtribes within family, showed data high support for among major lineages, were able provide resolution more recent radiations. Overall, molecular resources open new perspectives study phylogeny at taxonomical levels identification factors underlying diversification group.

Language: Английский

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Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation ofProteaL.

American Journal of Botany, Journal Year: 2017, Volume and Issue: 104(1), P. 102 - 115

Published: Jan. 1, 2017

PREMISE OF THE STUDY: Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with divergence result multiple gene tree histories. We combine anchored enrichment next‐generation sequencing species analyses to produce a robust estimate of the genus Protea (Proteaceae), an iconic radiation South Africa. METHODS: sampled individuals within 59 out 112 and 6 outgroup for total 163 individuals, obtained sequences 498 low‐copy, orthologous nuclear loci using phylogenomics. compare several approaches building trees, explore tree–species discrepancies determine whether poor resolution reflects lack informative sites, incomplete lineage sorting, or hybridization. KEY RESULTS: Phylogenetic estimates from are similar one another recover previously well‐supported clades , addition providing hypotheses poorly resolved intrageneric relationships. Individual trees markedly different trees. Nonetheless, indicate that differences among occur primarily concerning supported by branches. CONCLUSIONS: Species methods hundreds provided strong support many unresolved . In cases where particular remains low, these appear arise few sites information rather than strongly disagreement

Language: Английский

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