Collections‐based science in the 21st Century

Journal of Systematics and Evolution, Journal Year: 2018, Volume and Issue: 56(3), P. 175 - 193

Published: April 4, 2018

Abstract Discoveries from collections‐based science change the way we perceive ourselves, our environment, and place in universe. The 18 th Century saw beginning of formal classification with Linnaeus proposing a system to classify all life. 19 ushered age exploration as naturalists undertook large‐scale collecting expeditions leading major scientific advances (the founding Physical Geography, Meteorology, Ecology, Biogeography, Evolution) challenging long held beliefs about nature. In 20 collections were central paradigm shifts, including theories Continental Drift Phylogenetic Systematics; Molecular Phylogenetics added testable hypotheses, computerized specimen records gave rise field Biodiversity. first 15 years 21 st have seen tree‐thinking pervade life sciences, emergence Evolutionary Medicine, new Food Safety methods. More are on way: (i) Open access large amounts data & images, (ii) Linking climate phylogenies global scale, (iii) Production vast quantities genomic allowing us address big evolutionary questions. As result people see themselves not center things but rather part complex It is essential that integrate discoveries knowledge past (e.g., collections) order understand this planet inhabit. To ensure health must come together plan for future.

Language: Английский

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The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Diversity, Journal Year: 2022, Volume and Issue: 14(3), P. 213 - 213

Published: March 13, 2022

DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid effective tool for species identification. The growth barcodes as resource biologists followed advances in computational sequencing technology that have enabled high-throughput applications. global barcode database is expanding to represent diversity on Earth thanks efforts international consortia biological collections. Today, instrumental advancing our understanding how evolve, they interact, we can slow down their extirpation extinction. This review focuses current applications sequences address fundamental lines research, well new which will play central role.

Language: Английский

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Towards a multisensor station for automated biodiversity monitoring

Basic and Applied Ecology, Journal Year: 2022, Volume and Issue: 59, P. 105 - 138

Published: Jan. 7, 2022

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts temperature, transformations land-use, or energy budget systems. While latter processes easily quantifiable, documentation loss biodiversity community structure is more difficult. Changes organismal abundance diversity barely documented. Censuses species usually fragmentary inferred often spatially, temporally ecologically unsatisfactory simple lists for individual study sites. Thus, detrimental global their drivers remain unrevealed. A major impediment to monitoring lack human taxonomic expertise that implicitly required large-scale fine-grained assessments. Another amount personnel associated costs needed cover scales, inaccessibility remote but nonetheless affected areas. To overcome these limitations we propose a network Automated Multisensor stations Monitoring Diversity (AMMODs) pave way new generation assessment centers. This combines cutting-edge technologies with informatics expert systems conserve knowledge. Each AMMOD station autonomous samplers insects, pollen spores, audio recorders vocalizing animals, sensors volatile organic compounds emitted plants (pVOCs) camera traps mammals invertebrates. AMMODs largely self-containing have ability pre-process data (e.g. noise filtering) prior transmission receiver storage, integration analyses. Installation on sites difficult access require sophisticated challenging system design optimum balance between power requirements, bandwidth transmission, service, operation under all environmental conditions years. An important prerequisite automated identification databases DNA barcodes, animal sounds, pVOCs, images used as training identification. thus become key component advance field research policy delivering at an unprecedented spatial temporal resolution.

Language: Английский

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Medicinal plants meet modern biodiversity science

Current Biology, Journal Year: 2024, Volume and Issue: 34(4), P. R158 - R173

Published: Feb. 1, 2024

Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study medicinal plants combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, ethnopharmacology is poised facilitate new breakthroughs in science, including pharmacological discoveries rapid advancements health well-being. Such research leverages data spanning space, time, species associated with plant evolution, genomics, metabolomic trait diversity, all which build heavily on traditional Indigenous knowledge. contrasts sharply most well-funded successful during last half-century, which, despite notable advancements, has greatly oversimplified dynamic relationships between humans, kept hidden larger narratives about these relationships, overlooked potentially important into life-saving medicines. We suggest people should be viewed as partners whose relationship involves complicated poorly explored set (socio-)ecological interactions not only domestication but also commensalisms mutualisms. short, are just chemical factories extraction exploitation. Rather, they may symbiotic shaped modern societies, improved health, extended lifespans.

Language: Английский

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Progress in the use of DNA barcodes in the identification and classification of medicinal plants

Ecotoxicology and Environmental Safety, Journal Year: 2020, Volume and Issue: 208, P. 111691 - 111691

Published: Nov. 28, 2020

DNA barcoding is an emerging molecular identification and classification technology that has been applied to medicinal plants since 2008. The application of this technique greatly ensured the safety effectiveness materials. In paper, we review some related technologies over past 10 years with respect improving our knowledge plant authentication. From single locus-based barcodes combined markers genome-scale levels, contribute more genetic information. At same time, other technologies, such as high-resolution melting (HRM), have barcoding. With development next-generation sequencing (NGS), metabarcoding also shown identify species in mixed samples successfully. As a widely used effective tool, will become useful time field plants.

Language: Английский

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The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Plants, Journal Year: 2020, Volume and Issue: 9(4), P. 432 - 432

Published: April 1, 2020

Genome skimming has the potential for generating large data sets DNA barcoding and wider biodiversity genomic studies, particularly via assembly annotation of full chloroplast (cpDNA) nuclear ribosomal (nrDNA) sequences. We compare success genome skims 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried mainly European Alps Carpathians. Overall, we were able to assemble 67% samples nrDNA cluster 86%. Average insert length, cover cpDNA rDNA considerably higher than herbarium-preserved material. However, complete plastid genomes still assembled 54% compared 70% samples. Moreover, there was comparable recovery coding genes both tissue sources (121 118 material) only minor differences in standard barcodes between (89% ITS2, 96% matK rbcL) material (87% 98% rbcL). The rate > 90% all three markers 1034 1036 genera 160 families, Boraginaceae worked poorly, 7 failing. Our study shows that large-scale are feasible work well across most land plant families tested, independently type. It is therefore an efficient method increasing availability support a multitude downstream applications.

Language: Английский

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Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Molecular Ecology Resources, Journal Year: 2021, Volume and Issue: 22(1), P. 404 - 414

Published: July 26, 2021

Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, fail to discriminate among species in many groups. Genome skimming recover complete genome sequences arrays has been proposed as a solution address these resolution limitations. However, few studies have empirically tested what gains are achieved practice. Of particular interest is whether adding substantially more characters will lead an increase discriminatory power, or the limitations standard fundamentally due genomes not tracking boundaries. To this, we used near-complete nuclear ribosomal from Rhododendron compared discrimination success with barcodes. We sampled 218 individuals representing 145 this species-rich taxonomically difficult genus, focusing global biodiversity hotspots Himalaya-Hengduan Mountains. Only 33% were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% sequences. The vast majority additional characters. Thus, despite previous showing asymptote beyond 3-4 results that demonstrable power possible extensive data. gains, remain unresolved, also reinforce need access multiple unlinked loci obtain transformative plants.

Language: Английский

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Plant Genetic Diversity Studies: Insights from DNA Marker Analyses

International Journal of Plant Biology, Journal Year: 2024, Volume and Issue: 15(3), P. 607 - 640

Published: July 8, 2024

The plant adaptation response to a changing environment depends on the genetic diversity level it possesses. Genetic and thorough understanding of population indices are pivotal for decoding dynamic environmental stressors. development polymerase chain reaction (PCR)-based molecular markers enables comprehensive analyses precise detection individuals groups with unique variations. Various have been employed assess diversity, examine structure, delineate cluster patterns within among populations. DNA revolutionize studies by allowing detailed variations, including economically significant trait-influencing genes. Despite their simplicity, they offer high reproducibility, ensuring accurate estimations variation. Integrating multiple marker systems advanced high-throughput sequencing techniques is poised enhance management depleting resources providing picture at genome-wide level. This review explores diverse markers, elucidating advantages limitations, highlights impact evaluating structure plants.

Language: Английский

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Genetic diversity of closely related Calligounum species collected from Saudi habitats by analyzing the matK and rpoC1 genes, and SCoT and IRAP markers

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 13, 2025

Abstract The genus Calligonum L. Her ( Polygonaceae ) comprises 158 species with widespread distribution in regions such as India, China, North Africa, Pakistan, Afghanistan, Saudi Arabia, and South Europe. is a prominent shrubby psammophyte found deserts, known for its traditional medicinal uses. aim of this study to use Start Codon Target (SCoT) Inter-Retrotransposon Amplified Polymorphism (IRAP) markers evaluate the genetic diversity comosum tetrapterum Arabia. In addition, it uses raxmlHPC algorithm DNA barcoding techniques (matK rpoC1) examine phylogenetic relationships. SCoT IRAP revealed distinct patterns, clustering based on their similarities. matK rpoC1 genes provided valuable insights into evolutionary relationships within species. Phylogenetic analyses highlighted well-supported structures outgroup sequences showing early divergence. Conserved motifs analysis confirmed presence shared both isolated identified genes, validating potential biomarkers. This comprehensive enhances our understanding species’ relationships, contributing information taxonomic classification molecular marker validation. We are first add sequence gene Gen-Bank. conserved underscore applications various fields, including medicine biodiversity conservation.

Language: Английский

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Chloroplast Genome Evolution of Hamamelidaceae at Subfamily Level

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: March 27, 2025

ABSTRACT The Hamamelidaceae is significant for its contributions to construction, furniture making, and ornamental use, including 26 genera 119 species. However, complete chloroplast genome sequences of species have been reported less frequently. In this study, five were newly sequenced, seven others available genomes added compare the evolution in at subfamily level. results indicated that size ranged from 158,116 159,941 bp, encoding 79 81 protein‐coding genes, four ribosomal RNA 30 31 transfer genes. A robust phylogenetic tree was obtained using genomes, supporting all formed a monophyletic group divided into subfamilies. Exbucklandioideae first diverged within Hamamelidaceae, followed by Mytilarioideae, Disanthoideae, Hamamelidoideae, which clade. Furthermore, three new potential DNA barcodes provided: trnH‐psbA , psbJ‐petA ycf1 . This study confirms data provide more accurate confident resolution relationships Hamamelidaceae. These genomic not only enhance understanding but also better

Language: Английский

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