Advancing DNA Barcoding and Metabarcoding Applications for Plants Requires Systematic Analysis of Herbarium Collections—An Australian Perspective

Frontiers in Ecology and Evolution, Journal Year: 2018, Volume and Issue: 6

Published: Sept. 13, 2018

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realise the full potential of barcoding plants, particularly its application to metabarcoding mixed-species environmental samples, systematic sequencing reference collections is required using an augmented set loci, applied according agreed data generation analysis standards. The largest most complete are held in herbaria. Australia globally significant flora that well sampled expertly curated by herbaria, coordinated through Council Heads Australasian Herbaria. There exists tremendous opportunity provide comprehensive taxonomically robust database plant applications undertaking entire utilising existing herbarium material. In this paper, we review development consider requirements system. We analysed current availability Australian recommend priority taxa inclusion highlight future urge large-scale be undertaken promise metabarcoding, propose curation should become national investment priority.

Language: Английский

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Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome

New Phytologist, Journal Year: 2017, Volume and Issue: 214(4), P. 1408 - 1422

Published: March 9, 2017

I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: Tropical rainforest (TRF) is the most species-rich terrestrial biome on Earth, harbouring just under half of world's plant species in c. 7% land surface. Phylogenetic trees provide important insights into mechanisms underpinning TRF hyperdiversity that are complementary to those obtained from fossil record. studies diversity have mainly focused whether this an evolutionary 'cradle' or 'museum', emphasizing speciation and extinction rates. However, other explanations, such as age, immigration ecological limits, must also be considered. We present a conceptual framework for addressing drivers diversity, review tested them with phylogenetic data. Although surprisingly few number, these point old age TRF, low high rates credible hyperdiversity. There less evidence but cannot dismissed owing limited number studies. Rapid methodological developments DNA sequencing, macroevolutionary analysis integration phylogenetics disciplines may improve our grasp future. advances critically dependent fundamental systematic research, yielding numerous, additional, well-sampled phylogenies lineages.

Language: Английский

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Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 9

Published: Jan. 9, 2019

Targeted enrichment and sequencing of hundreds nuclear loci for phylogenetic reconstruction is becoming an important tool plant systematics evolution. Annonaceae a major pantropical family with 109 genera ca. 2450 species, occurring across all minor tropical forests the world. Baits were designed by transcriptomes five species from two largest subfamilies. Orthologous identified. The resulting baiting kit was used to reconstruct relationships at different levels using concatenated gene tree approaches: wide analysis sampling 65 level tribe Piptostigmateae 29 multiple individuals per species. DNA extraction undertaken mainly on silicagel dried leaves, samples herbarium leaves. Our targets 469 exons (364,653 bp sequence data), successfully capturing sequences Annonaceae. Silicagel worked equally well. We present first time gene-based generic based 317 supercontigs. Results confirm previous chloroplast studies. However, several new are found discussed. show significant differences in branch lengths between large subfamilies Annonoideae Malmeoideae. A tribe, Annickieae, erected containing single African genus Annickia. also reconstructed well resolved species-level Piptostigmteae tribe. useful reconstructing supported within taxonomic levels. genome concordant plastome information few exceptions. Moreover, we find that substitution rate heterogeneity compartment, not just plastomes ribosomal as previously shown. results have implications understanding biogeography, molecular dating evolution

Language: Английский

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A new classification of Cyperaceae (Poales) supported by phylogenomic data

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 59(4), P. 852 - 895

Published: May 9, 2021

Abstract Cyperaceae (sedges) are the third largest monocot family and of considerable economic ecological importance. Sedges represent an ideal model to study evolutionary biology due their species richness, global distribution, large discrepancies in lineage diversity, broad range preferences, adaptations including multiple origins C 4 photosynthesis holocentric chromosomes. Goetghebeur′s seminal work on published 1998 provided most recent complete classification at tribal generic level, based a morphological inflorescence, spikelet, flower, embryo characters, plus anatomical other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after last comprehensive family, we present first family‐wide phylogenomic targeted sequencing Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads included analyses. Informed by this backbone phylogeny, new tribal, subtribal, levels is proposed. The majority previously recognized suprageneric groups supported, time, establish support tribe Cryptangieae as clade genus Koyamaea . We provide taxonomic treatment identification keys diagnoses 2 subfamilies, 24 tribes, 10 subtribes, basic information 95 genera. includes five subtribes Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, Oreobolinae.

Language: Английский

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Defining Coalescent Genes: Theory Meets Practice in Organelle Phylogenomics

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(2), P. 476 - 489

Published: June 28, 2021

The species tree paradigm that dominates current molecular systematic practice infers trees from collections of sequences under assumptions the multispecies coalescent (MSC), is, there is free recombination between and no (or very low) within them. These genes (c-genes) are thus defined in an historical rather than sense can theory be as large entire genome or small a single nucleotide. A debate about how to define c-genes centers on contention nuclear gene used many analyses undergo too much recombination, such their introns comprise multiple c-genes, violating key assumption MSC. Recently similar argument has been made for plastid (e.g., chloroplast) mitochondrial genomes, which last 30 more years have considered represent c-gene purposes phylogeny reconstruction because they nonrecombining sense. Consequently, it suggested these genomes should analyzed using methods treat genes-over 70 protein-coding case most (plastomes)-as independent estimates phylogeny, contrast usual concatenation, appropriate generating trees. However, although certainly occurs plastome, recognized since 1970's, unlikely phylogenetically relevant. This historically effective only occur when plastomes with incongruent histories brought together same plastid. plastids sort rapidly into different cell lineages rarely fuse. Thus, biology, plastome canonical average multi-intron mammalian gene. continue treated estimate underlying genome. implications this long-held insight systematics studies phylogenomic era explored. [c-gene; gene; concatalescence; organelle genome; plastome; recombination; tree.].

Language: Английский

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Herbaria as Big Data Sources of Plant Traits

International Journal of Plant Sciences, Journal Year: 2021, Volume and Issue: 183(2), P. 87 - 118

Published: Oct. 21, 2021

Herbarium specimens have long been a cornerstone of taxonomic research but are only recently being recognized for their potential as source spatially and temporally extensive data on plant functional traits. Many researchers in trait-based disciplines, including ecologists evolutionary biologists alike, remain surprisingly unaware this powerful use herbaria. This review brings together disparate studies to synthesize the past, current, future uses trait sources, answering following questions. First, what insights using (including traits measured, approaches used, questions answered) made date? Second, new contributions global databases recent advancements such machine learning high-throughput phenotyping) can be from herbarium specimens? And third, how inherent limitations collection biases addressed when unanticipated ways analytical improved methods collecting)? I conclude by identifying is needed foster herbaria big sources Most notably, collecting must continued, expanded beyond predominantly systematists, intentionally revised with downstream measurements mind. Furthermore, community-wide standards integrate otherwise disconnected directly link newly derived back specimen records. Specimens serve reliable (and necessary) phenotypic data, enabling us answer across phylogenetic, temporal, spatial dimensions that not possible answer. Herbaria should embraced centers research.

Language: Английский

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Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

Systematic Entomology, Journal Year: 2021, Volume and Issue: 46(3), P. 649 - 671

Published: March 29, 2021

Abstract Museum collections around the world contain billions of specimens, including rare and extinct species. If their genetic information could be retrieved at a large scale, this would dramatically increase our knowledge taxonomic diversity information, support evolutionary, ecological systematic studies. We here present target enrichment kit for 2953 loci in 1753 orthologous nuclear genes + barcoding region cytochrome C oxidase 1, Lepidoptera demonstrate its utility to obtain number from dry, pinned museum material collected 1892 2017. sequenced enriched libraries 37 specimens across order Lepidoptera, many higher taxa not yet included high‐throughput molecular studies, showing that can used generate comparable data order, provides resolution both shallower deeper nodes. The filtered datasets (172 taxa, 234 464 amino acid positions corresponding nucleotides 1835 CDS regions) were infer phylogeny which is largely congruent topology recent phylogenomic but with addition some key taxa. furthermore TEnriAn (Target Enrichment Analysis) workflow processing combining enrichment, transcriptomic genomic data.

Language: Английский

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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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Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

PhytoKeys, Journal Year: 2022, Volume and Issue: 205, P. 3 - 58

Published: Aug. 22, 2022

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically economically important group trees, shrubs lianas a pantropical distribution. Despite major advances last few decades towards aligning clades across Caesalpinioideae, generic delimitation remains state considerable flux, especially mimosoid clade. We test monophyly via phylogenomic analysis 997 nuclear genes sequenced targeted enrichment (Hybseq) for 420 147 currently recognised subfamily. show that 22 are non-monophyletic or nested other non-monophyly concentrated clade where 25% 90 found to be non-monophyletic. suggest two main reasons this pervasive non-monophyly: (i) extensive morphological homoplasy we document here handful traits and, particularly, repeated evolution distinctive fruit types were historically emphasised delimiting (ii) artefact lack taxonomic syntheses sampling previous phylogenies consequent failure identify span Old World New conversely amphi-Atlantic non-monophyletic, both which critical large Finally, discuss taxon era how assessing patterns gene tree conflict can provide additional insights into delimitation. This new framework provides foundations series papers reclassifying presented

Language: Английский

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Implications and future prospects for evolutionary analyses of DNA in historical herbarium collections

Botany Letters, Journal Year: 2018, Volume and Issue: 165(3-4), P. 409 - 418

Published: April 23, 2018

Global herbarium collections house a vast number of plant specimens stretching back over centuries. They include rare and extinct species, important historical collections, valuable type that could help to resolve long-standing taxonomic issues. Historical also provide unique windows into past evolutionary processes population histories do not exist with modern data alone. However, because the DNA in such is often degraded scarce, manipulation analysis their genetic material can be challenging. Recent developments non-destructive sampling working very small quantities genomic DNA, especially next-generation sequencing bioinformatic ancient now make majority potentially accessible phylogenetic, genetic, barcoding studies. For example, studies from long time series Ipomoea batatas Anacamptis palustris revealed linkages between anthropogenic activity changes haplotype distribution. These enable identification genes under recent selection genomes both plants pathogens, as was shown for Phytophthora infestans, microbial pathogen Solanum tuberosum. Here, we summarize major challenges using review integrating specimens. We expect future use genomic, metagenomic, approaches to: investigate how populations respond environmental change; infer temporal diversity; identify selection; epidemics.

Language: Английский

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