From barcodes to genomes: extending the concept of DNA barcoding

Molecular Ecology, Journal Year: 2016, Volume and Issue: 25(7), P. 1423 - 1428

Published: Jan. 28, 2016

Abstract DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of establishing massive scale databases for few barcode loci is continuing to change our understanding species diversity patterns, and continues enhance human abilities distinguish among species. Capitalizing the developments next generation sequencing technologies decreasing costs genome sequencing, there now opportunity concept be extended new kinds genomic data. We illustrate benefits capacity do this, also note constraints barriers overcome before it truly scalable. advocate twin track approach: (i) continuation acceleration global efforts build reference library life earth using standard barcodes (ii) active development application skimming augment approach.

Language: Английский

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Telling plant species apart with DNA: from barcodes to genomes

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2016, Volume and Issue: 371(1702), P. 20150338 - 20150338

Published: Aug. 2, 2016

Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent critically important component terrestrial biodiversity-yet many tens thousands species await discovery, plant identification remains substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, provide short summary the strengths limitations DNA barcoding for addressing these issues. Secondly, discuss options enhancing current barcodes, focusing on increasing discriminatory power via either gene capture nuclear markers genome skimming. The former has advantage establishing defined set target loci maximizing efficiency sequencing effort, data storage analysis. challenge developing probe large numbers that works over sufficient phylogenetic breadth. Genome skimming using existing protocols being backward compatible with barcodes; depth sequence coverage can be increased as costs fall. Its non-targeted nature does, however, present major informatics upscaling to sample sets.This article part themed issue 'From barcodes biomes'.

Language: Английский

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Next-generation biology: Sequencing and data analysis approaches for non-model organisms

Marine Genomics, Journal Year: 2016, Volume and Issue: 30, P. 3 - 13

Published: May 14, 2016

As sequencing technologies become more affordable, it is now realistic to propose studying the evolutionary history of virtually any organism on a genomic scale. However, when dealing with non-model organisms not always easy choose best approach given specific biological question, limited budget, and challenging sample material. Furthermore, although recent advances in technology offer unprecedented opportunities for research organisms, they also demand awareness from researcher regarding assumptions limitations each method. In this review we present an overview current methods used typical high-throughput data analysis pipelines. Subsequently, contextualize DNA within their applications biology. We include tips managing unconventional material, comparative population genetic approaches that do require fully assembled genomes, advice how deal low depth data.

Language: Английский

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Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Science Advances, Journal Year: 2023, Volume and Issue: 9(7)

Published: Feb. 17, 2023

Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment geography as two principal axes determining the distribution of groups organisms, laying foundations for biogeography over subsequent 200 years, yet relative importance these remains unresolved. Leveraging phylogenomic global species data Mimosoid legumes, a pantropical plant clade c. 3500 species, we show that water availability gradient from deserts to rain forests dictates turnover lineages within continents across tropics. We demonstrate 95% speciation occurs precipitation niche, showing profound phylogenetic niche conservatism, lineage boundaries coincide with isohyets precipitation. reveal similar patterns on different continents, implying evolution dispersal follow universal processes.

Language: Английский

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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification

PhytoKeys, Journal Year: 2024, Volume and Issue: 240, P. 1 - 552

Published: April 3, 2024

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It an ecologically economically important group formed mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas shrubs, which has a global distribution, occurring on every continent except Antarctica. Following recent re-circumscription 15 genera as presented in Advances Legume Systematics 14, Part 1, using basis phylogenomic analysis 997 nuclear gene sequences for 420 all but five currently recognised subfamily, we present new higher-level classification subfamily. The comprises eleven tribes, are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 / 223 species), Campsiandreae LPWG (2 5–22), Cassieae Bronn (7 695), Ceratonieae (4 6), Dimorphandreae Benth. 35), Erythrophleeae /13), Gleditsieae Nakai (3 20), Mimoseae (100 3510), Pterogyneae (1 1), Schizolobieae (8 42–43), Sclerolobieae & Hook. f. (5 113). Although many these lineages have been named past, tribes informal generic groups, their circumscriptions varied widely changed over past decades, such described here differ membership those previously recognised. Importantly, approximately 3500 100 former Mimosoideae now placed reinstated, newly circumscribed, tribe Mimoseae. Because size ecological importance tribe, also provide clade-based system includes 17 lower-level clades. Fourteen remain unplaced clades: eight resolved two grades six phylogenetically isolated monogeneric lineages. In addition classification, key genera, morphological descriptions notes diversity growth forms, foliage, flowers fruits illustrated each genus distribution map, based quality-controlled herbarium specimen localities. A glossary specialised terms used legume morphology provided. This provides solid communication framework downstream analyses biogeography, trait evolution diversification, well taxonomic revision still understudied

Language: Английский

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Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Frontiers in Plant Science, Journal Year: 2015, Volume and Issue: 6

Published: Sept. 17, 2015

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical ecological settings; neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness the result recent radiations. Understanding evolutionary trajectories mechanisms underlying these demands much greater phylogenetic resolution than currently available for groups. The tree genus Inga (Leguminosae) good example, with ~300 extant crown age 2-10 MY, yet over 6kb plastid nuclear DNA sequence data gives only poor among species. Here we explore use larger-scale gene obtained though targeted enrichment to increase within Inga. Transcriptome from three were used select 264 loci sequencing. Following quality control remove probable paralogs data, final dataset comprised 259,313 bases 194 24 accessions representing 22 an outgroup (Zygia). Bayesian phylogenies reconstructed using either all concatenated or subset 60 gene-tree/species-tree approach yielded highly resolved phylogenies. We coalescent approaches show same also have power discriminate alternative within-species population histories widespread I. umbellifera. In application, simplifies informatics challenge identifying orthologous associated de novo genome conclude provides large volumes phylogenetically-informative required resolve relationships radiations, both at level phylogeographic studies.

Language: Английский

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Dispersal assembly of rain forest tree communities across the Amazon basin

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 114(10), P. 2645 - 2650

Published: Feb. 17, 2017

Significance The Amazon is largely covered by contiguous rain forest. Nevertheless, previous studies have suggested that past geological and climatic events, as well limited seed dispersal, may restricted the movement of tree lineages across Amazon. Using a phylogenetic approach, we show dispersal into local communities larger regions in appears to not been on evolutionary timescales, but instead, assembled from These results contrast with those seasonally dry tropical forests, where closely related species are clustered geographic space. Furthermore, our suggest role for an initiator isolation might lead speciation Amazonian trees.

Language: Английский

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Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above

New Phytologist, Journal Year: 2018, Volume and Issue: 220(2), P. 636 - 650

Published: July 17, 2018

Summary Reconstructing phylogenetic relationships at the micro‐ and macroevoutionary levels within same tree is problematic because of need to use different data types analytical frameworks. We test power target enrichment provide resolution based on DNA sequences from above species populations, using a large herbarium sampling Euphorbia balsamifera (Euphorbiaceae) as case study. Target with custom probes was combined genome skimming (Hyb‐Seq) sequence 431 low‐copy nuclear genes partial plastome . used supermatrix, multispecies‐coalescent approaches, Bayesian dating estimate divergence times. , disjunct Rand Flora‐type distribution opposite sides Africa, comprises three well‐supported subspecies: western Sahelian sepium sister eastern African‐southern Arabian adenensis Macaronesian‐southwest Moroccan Lineage times support Late Miocene Pleistocene diversification climate‐driven vicariance explain Flora pattern. show that designed genomic resources taxa not directly related focal group are effective in providing deep shallow evolutionary levels. Low capture efficiency samples increased proportion missing but did bias estimation or branch lengths.

Language: Английский

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Retrieval of hundreds of nuclear loci from herbarium specimens

Taxon, Journal Year: 2016, Volume and Issue: 65(5), P. 1081 - 1092

Published: Oct. 1, 2016

Abstract Herbaria are unparalleled collections of biodiversity information representing the world's flora. However, this treasure has remained largely inaccessible to genetic studies, frequently limited by low yields poor‐quality DNA. Next‐generation sequencing (NGS) transformed every field biological research. The different strategies for accessing data using NGS changing direction research—we no longer constrained a relatively small number markers non‐model organisms, time and cost sample sizes, or incomplete datasets due recalcitrant DNA extractions PCR amplification failure. Here we show that targeted enrichment through hybrid capture can be used generate hundreds kilobases nuclear sequence Neotropical genus Inga , from herbarium specimens as old 180 years little 16 ng degraded

Language: Английский

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Tackling Rapid Radiations With Targeted Sequencing

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 10

Published: Jan. 9, 2020

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount genomic data now available statistical tools analyze provide unprecedented power for inference. Targeted sequencing has emerged as a strong tool estimating species trees in the face rapid radiations, lineage sorting introgression. Evolutionary relationships Cyperaceae been studied mostly using Sanger until recently. Despite ample taxon sampling, many genera remain poorly understood, hampered diversification rates that outpace mutation loci used. C4 Cyperus Clade genus particularly difficult resolve. Previous based on limited set markers resolved among C3 photosynthetic pathway, but not taxa. We test ability two targeted kits Clade, universal Angiosperms-353 kit Cyperaceae-specific kit. Sequences were recovered from generated with both used investigate overlap between relative efficiency general custom approaches. shallow-level was tested summary tree method concatenated maximum likelihood approach. High resolution support are obtained approaches, high levels missing disproportionately impact latter. provides new insights into evolution morphology demonstrating example former segregate Alinula is polyphyletic its seeming morphological integrity. An unexpected result margaritaceus-Cyperus niveus complex comprises clade separate sister core Clade. Our results demonstrate family-specific do necessarily more than those kit, different can often be merged downstream analyses. Moreover, our study contributes growing consensus powerful resolving radiations.

Language: Английский

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