Mining museums for historical DNA: advances and challenges in museomics

Trends in Ecology & Evolution, Journal Year: 2021, Volume and Issue: 36(11), P. 1049 - 1060

Published: Aug. 26, 2021

Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion extinction, discovering species to science, resolving evolutionary relationships, investigating epigenetic effects, determining origins infectious diseases. However, development best-practices in isolating, processing, analyzing hDNA remain under-explored, due substantial diversity specimen preparation types, tissue sources, archival ages, collecting histories. Thus, for reach its full potential, justify destructive sampling rarest more experimental work using time-series collections, improved methods correct data asymmetries biases degradation are required.

Language: Английский

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Genome skimming herbarium specimens for DNA barcoding and phylogenomics

Plant Methods, Journal Year: 2018, Volume and Issue: 14(1)

Published: June 5, 2018

The world's herbaria contain millions of specimens, collected and named by thousands researchers, over hundreds years. However, this treasure has remained largely inaccessible to genetic studies, because both generally limited success DNA extraction the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities prospects for historical have changed dramatically, as most NGS methods are actually designed taking short fragmented molecules templates. As a practical test routine recovery rDNA plastid genome sequences from herbarium we sequenced 25 specimens up 80 years old 16 different Angiosperm families. Paired-end reads were generated, yielding successful assemblies 23 species nuclear rDNAs 24 species, respectively. These data showed that skimming can be used generate genomic information using little 500 pg starting plastome is feasible cost-effective (compare Sanger or plastome-enrichment approaches), performed sample destruction.

Language: Английский

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The Global Museum: natural history collections and the future of evolutionary science and public education

PeerJ, Journal Year: 2020, Volume and Issue: 8, P. e8225 - e8225

Published: Jan. 28, 2020

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits public programming by hosting rich communities of amateurs, students, researchers at all stages their careers, they can provide a place-based window to focus on integration science discovery, as well locus community engagement. At the same time, like synthesis radio telescope, when joined together through emerging digital resources, global (the 'Global Museum') is more than sum its parts, allowing insights answers diverse biological, environmental, societal questions scale, across eons spanning vast diversity Tree Life. We argue that, whereas natural collections began with describing peculiarities species Earth, now increasingly leveraged in new ways that significantly expand impact relevance. These directions include possibility ask new, often basic applied science, such biomimetic design, contributing solutions climate change, health food security challenges. As institutions, have long been incubators cutting-edge biology while simultaneously providing core infrastructure present future needs. Here we explore how intersection between pressing issues environmental human rapid technological innovation reinforced relevance museum collections. do this examples thought both broader academic scientists evolving role museums. also identify challenges realization full potential Global Museum society discuss critical need grow these then mapping modelling data (including approaches discovery), main projects, platforms databases enabling growth. Finally, aim improve relevant protocols long-term storage specimens tissues, ensuring proper connection tomorrow's technologies hence further increasing

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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Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: Sept. 18, 2019

The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained herbarium specimens was difficult until arrival high-throughput sequencing approaches, which can be applied to low quantities severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise capture genomic regions interest for sequencing. In this study on herbariomics, we used targeted approach Angiosperms353 universal probe set recover up 351 nuclear genes 435 are 204 years old span breadth angiosperm diversity. We show average 207 were successfully retrieved although mean number target efficiency is significantly higher silica gel-dried Forty-seven recovered a specimen critically St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium yield less high-molecular-weight than quality declines with sample age, negatively correlated efficiency. Climate, taxon-specific traits, collection strategies additionally impact sequence recovery. also detected taxonomic bias outcomes 10 most numerous families investigated depth. recommend (1) distributed wet tropical climates, should preferentially; (2) seasonally dry similar results, either used; (3) traits explored established effective optimisation studies specimens; (4) all sheets should, future, annotated details preservation method (5) long-term storage stable, low-humidity, low-temperature environments; (6) probes, such as Angiosperms353, closely new barcoding will ensure better exploitation traditional Sanger approaches.

Language: Английский

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Digitization of herbaria enables novel research

American Journal of Botany, Journal Year: 2017, Volume and Issue: 104(9), P. 1281 - 1284

Published: Sept. 1, 2017

As botanists, we recognize that herbarium specimens document spatial and temporal patterns of plant diversity. But they may also tell stories beyond the plants themselves—about how a specimen have languished for decades in obscurity until botanist with keen eye recognized it as new species (Ziziphus celata; see, e.g., Judd Hall, 1984; image, see https://www.floridamuseum.ufl.edu/scripts/dbs/herbs_project/herbsproject/herbs_pub_proc.asp?accno=136888&FamSys=A&output_style=Report_type&trys=2) or heroics required to relocate nature (e.g., Shortia galacifolia; https://www.idigbio.org/content/portal-curiosities-asa-gray-and-quest-shortia-galacifolia-%E2%80%93-case-study-importance) metamorphosing collections themselves, yielding data undreamt when were collected Inga umbellifera; Hart et al., 2016; http://elmer.rbge.org.uk/bgbase/vherb/bgbasevherb.php?cfg=bgbase/vherb/fulldetails.cfg&specimens_specimen__num=369514). These Ziziphus (or Pseudoziziphus!), Shortia, represent just handful estimated 350,000,000 deposited world's 3400 herbaria (Index Herbariorum, http://sciweb.nybg.org/Science2/IndexHerbariorum.asp). Collected over past four centuries, vegetation, including has changed response human activities population expansion, provide basis scientific names form type specimens. Until recently, under lock key accessible only small number specialists, but digitization is now global enterprise, images are emerging digital from around world. Digitization—that is, electronic capture data, images—began ago some databasing basic information about (scientific name, collector, date collection, locality, etc.). Through innovations database design usability, application standards natural history DarwinCore; Wieczorek 2012), improved methods imaging Tegelberg 2014), development high-throughput workflows (as implemented, example, Paris Herbarium; https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/02_SPNHC2014_chagnoux.pdf), pace increased dramatically. The Global Plants Initiative (GPI; https://plants.jstor.org/), push digitize botanical specimens, demonstrated both will collaborative spirit leaders world feasibility large-scale, international, efforts. In many ways, GPI set stage remarkable resources available today. Data aggregators—such Biodiversity Information Facility (GBIF), Atlas Living Australia (ALA), U. S. Geological Survey's portal (Biodiversity Serving Our Nation; BISON), iDigBio (Integrated Digitized Biocollections, funded by National Science Foundation (NSF); below)—provide biodiversity public using standardized terminology specified DarwinCore. Other national regional aggregators serve information, collectively these allow visualization analysis novel exciting ways. Although passed since first records databased made via internet, within few years sufficient numbers become innovative research. We at brink opportunities synthetic analyses connect digitized other (phylogenetic, climatological, genomic, etc.; Soltis Soltis, 2016) address questions biology longstanding perspectives larger scales. (www.idigbio.org) was founded 2011 collect share rapidly increasing volume flowing investments technology NSF. this writing, currently serves 105 million US international collections. Of these, approximately 50 records. Moreover, 22 media records, most which images, nearly 20 representing What resource research education—and more millions pipeline! When NSF began funding Advancing Digitization Collections Program 2011, community immediately emerged collaborative, organized network institutions shared goals digitizing joint efforts several projects, thematic networks, best practices been developed (Nelson 2015), continue spur digitization. Efforts develop an online Virtual Herbarium portal—with plant-specific resources, maps, checklists, literature, etc., access all iDigBio's records—are underway, anticipated completion 2018. Digital repositories fast, easy, cheap anyone Internet connection. While goal bringing museum out cabinets onto itself worthwhile reasons, real value lies uses images. Given collection element label typically captured databases, not surprising used study shifts phenology (that seasonal timing life-history events such flowering leaf-out) associated climate change Miller-Rushing 2006; 2014). For Primack (2008) time Massachusetts century half combination Henry David Thoreau's notes modern approach harvesting times bud burst increasingly phenological phylogenetic (see review Willis 2017). However, relied on visits herbaria; recent, rapid increase enables similar studies greater geographic scales, well remote areas Despite apparent utility research, clear without biases, accommodation biases intriguing avenues their own right (Davis 2015; Meyer 2016). grow, pulling together globe, potential given be sufficiently large ameliorate least arise purposes those collected. like can rich sources locality used, conjunction environmental generate distribution models (also referred ecological niche models). Accurate rely points, effectively (and sometimes only) achieved vast Such instrumental predicting responses being applied role speciation diploid polyploid levels Marchant Visger northern hemisphere, expect move northward higher elevations, if able, warming climate. predicted migrations complex hotspots, California, where along elevational gradients predict lower—and warmer—elevations rather than up mountains changing temperatures, following water availability temperature Rapacciuolo Florida, part state, southern end eastern deciduous forest, century, whereas central state—representing scrub habitats already hot dry—are southward, likely (Fig. 1). modeling further implications conservation, particularly phylogenies diversity J. M. Allen University New Hampshire, unpublished manuscript; Fig. 2). accomplished extracted examination physical greatly extends scope, scale, regions explored improves quality models, enabling would otherwise impossible. Maps showing vascular Florida based >500,000 Bioclim variables (Hijmans 2005), Maxent software (Phillips 2006). (A) Present 1500 (of 4200 species) construct models. (B) Changes 2050 relative present. Green indicate diversity, tan decreased present (C. C. Germain-Aubrey data). # = number. Map (from 1) phylogeny rbcL matK sequences manuscript, methods). Note areas, peninsular show low 1A) intermediate indicating divergent branches phylogeny. endemism hotspots 1); identified dividing endemic total use begins demonstrate data. Largely unexplored yet image identification Unger Carranza-Rojas 2017) large-scale 2017, discussion). resolution varies among (but note specifies minimum 600 dots per inch), untapped morphological characters functional traits, extraction traits enable multiple exploration. imagine able hundreds thousands score (whether systematic study), examine color infer pigment concentrations identifications, measure stomatal trichome densities, survey "paleoherbivory" insect damage fossil leaves, suggest few. High-throughput phenotyping images—via any (Gehan Kellogg, 2017)—can revolutionize ecology evolution ties phenomic integrate genotypes phenotypes. Beyond textual descriptions habitats, potentially mined words correspond features interest. Linking inferred databases TRY Plant Trait Database (https://www.try-db.org/de/de.php) yield powerful sets exploring range Refinement text-parsing algorithms, coupled ontologies Stucky 2016), likewise lead evolutionary Novel applications beginning appear. augmented literature-based medicinal (Souza Hawkins, Tools integration discoveries. And, course, roles play systematics, focus use. transforming, offer pressing societal problems related change, food security, conservation. Champions long promoted collections, and, technological breakthroughs imaging, molecular biology, genetics, herbaria, fine wine, seem time. I thank Mark Whitten, Dick Olmstead, Chuck Davis, Pete Hollingsworth inspiring discussions favorite Editor-in-Chief Pamela Diggle three anonymous reviewers helpful suggestions earlier draft manuscript. This work supported grant DBI-1547229.

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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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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Hyb-Seq for Flowering Plant Systematics

Trends in Plant Science, Journal Year: 2019, Volume and Issue: 24(10), P. 887 - 891

Published: Aug. 30, 2019

Language: Английский

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A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 10

Published: Feb. 21, 2020

High-throughput DNA sequencing techniques enable time- and cost-effective of large portions the genome. Instead annotating whole genomes, many phylogenetic studies focus effort on sets pre-selected loci, which further reduces costs bioinformatic challenges while increasing coverage. One common approach that enriches loci before is often referred to as target sequence capture. This technique has been shown be applicable greatly varying evolutionary depth. Moreover, it proven produce powerful, multi-locus datasets suitable for analyses. However, capture requires careful considerations, may affect success experiments. Here we provide a simple flowchart designing phylogenomic We discuss necessary decisions from identification final processing data. outline solutions related taxonomic scope, sample quality, available genomic resources projects. hope this review will serve useful roadmap carrying out successful studies.

Language: Английский

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