Genomics for monitoring and understanding species responses to global climate change

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 25(3), P. 165 - 183

Published: Oct. 20, 2023

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish species' potential adapt future environments. Understanding monitoring how organisms respond human-driven change is therefore major priority for conservation rapidly changing environment. Recent developments genomic, transcriptomic epigenomic technologies enabling unprecedented insights into evolutionary processes molecular bases adaptation. This Review summarizes methods that apply integrate omics tools experimentally investigate, monitor predict species communities wild cope with change, which by genetically adapting new conditions, through range shifts or phenotypic plasticity. We identify advantages limitations each method discuss research avenues would improve our understanding responses highlighting need holistic, multi-omics approaches ecosystem during Species can shifting their these responses.

Language: Английский

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Environmental DNA as an emerging tool in botanical research

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(2)

Published: Jan. 12, 2023

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species communities), means of elucidating biological interaction networks, window into understanding patterns biodiversity. However, only recently potential eDNA realized in botanical world. Here we synthesize state applications systems with emphases on aquatic, ancient, contemporary sediment, airborne systems, focusing both single-species approaches multispecies community metabarcoding. Further, describe how abiotic biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, relative abundance influence utilization interpretation results. Lastly, explore several areas opportunities for further development tools plants, advancing our knowledge efficacy, utility, cost-effectiveness, ultimately facilitating increased adoption analyses systems.

Language: Английский

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Deep-time paleogenomics and the limits of DNA survival

Science, Journal Year: 2023, Volume and Issue: 382(6666), P. 48 - 53

Published: Oct. 6, 2023

Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from preserved in sediments, will enable inference adaptive evolution, discovery unrecognized species, and exploration how glaciations, volcanism, paleomagnetic reversals demography community composition. In this Review, we explore state-of-the-art paleogenomics discuss key challenges, technical limitations, evolutionary divergence associated biases, need for more precise dating remains sediments. We conclude with improvements laboratory computational methods, emerging field expand range questions addressable using DNA.

Language: Английский

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Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

Cell, Journal Year: 2024, Volume and Issue: 187(14), P. 3541 - 3562.e51

Published: July 1, 2024

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin a female woolly mammoth (†Mammuthus primigenius) died 52,000 years ago retained its architecture. We use PaleoHi-C map chromatin contacts assemble genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, inactive X chromosome (Xi) superdomains persist. The active compartments in more closely resemble Asian elephant than other tissues. Our analyses uncover new biology. Differences compartmentalization reveal genes whose transcription was potentially altered mammoths vs. elephants. Mammoth Xi has tetradic architecture, not bipartite like human mouse. hypothesize that, shortly after this mammoth's death, sample spontaneously freeze-dried Siberian cold, leading glass transition preserved subfossils chromosomes at nanometer scale.

Language: Английский

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CRISPR-powered quantitative keyword search engine in DNA data storage

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 15, 2024

Despite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying stored is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which utilizes CRISPR-Cas12a rapidly generate visible fluorescence when target corresponding keyword present. SEEKER achieves quantitative text searching since growth rate intensity proportional frequency. Compatible with SEEKER, develop non-collision grouping coding, reduces size dictionary and enables lossless compression without disrupting original order texts. Using four queries, correctly identify keywords 40 files background ~8000 irrelevant terms. Parallel can be performed on 3D-printed microfluidic chip. Overall, provides approach conducting parallel over complete content simple implementation rapid result generation.

Language: Английский

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Genetic gains underpinning a little-known strawberry Green Revolution

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 19, 2024

Abstract The annual production of strawberry has increased by one million tonnes in the US and 8.4 worldwide since 1960. Here we show that expansion was driven genetic gains from Green Revolution breeding advances yields 2,755%. Using a California population with century-long history phenotypes hybrids observed coastal environments, estimate fruit 2,974-6,636%, counts 1,454-3,940%, weights 228-504%, firmness 239-769%. genomic prediction approaches, pinpoint origin to early 1950s uncover significant increases additive variation caused transgressive segregation phenotypic diversification. Lastly, most consequential breakthrough introduction photoperiod-insensitive, PERPETUAL FLOWERING 1970s doubled drove dramatic California.

Language: Английский

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Importance of eDNA taphonomy and sediment provenance for robust ecological inference: Insights from interfacial geochemistry

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(2)

Published: March 1, 2024

Abstract Retrieval of modern and ancient environmental DNA (eDNA) from sediments has revolutionized our ability to study past present ecosystems. Little emphasis been placed, however, on the fundamentals DNA–sediment associations in settings. Consequently, understanding mineralogic controls geochemical processes that take place interface, its implications for eDNA taphonomy provenance, remain extremely limited. Here, we apply interfacial principles elucidate how depositional stability different environments can influence interpretation identify possible interpretational biases arising neglecting mineral taphonomy. We use atomic force microscopy show interactions drive adsorption behavior outline increase scope resolution ecological interpretations by combining composition information with experimental data. bring concepts together propose integrate sediment provenance as well analysis improved reconstruction ecosystems monitoring provide a conceptual be addressed further applied enhance scope, resolution, accuracy reconstructions based

Language: Английский

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Targeting Terrestrial Vertebrates With eDNA: Trends, Perspectives, and Considerations for Sampling

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(1)

Published: Jan. 1, 2025

ABSTRACT Terrestrial vertebrates are experiencing worldwide population declines and species extinctions. To effectively conserve remaining populations species, rapid, cost‐effective, scalable methods needed to complement longstanding monitoring methods. Increasingly, environmental DNA (eDNA)‐based approaches being used for terrestrial vertebrate biomonitoring within a range of environments. However, as we move eDNA onto land, presented with new set challenges. This necessitates the development “best‐practice” sample collection guidelines systems purpose detecting vertebrates. address these needs, conducted systematic literature review 143 peer‐reviewed papers applying (excluding Lissamphibia) that were published between 2012 2023. We summarize use biomonitoring, focusing on study design field techniques. Over decade observe steady growth in annual number publications, 3 33 The majority reviewed studies targeted mammals temperate forest regions. While an equal focused metabarcoding approach assess community taxon composition and/or species‐specific detection methods, novel uses increasingly published. These include animal behavior genetics. record three types sampling strategies, eight different substrate types, seven preservation suggesting there is no “one size fits all” eDNA‐based methodology when With multitude aims, across environments, target organisms ecologies, standardization extremely challenging. table known factors influencing Furthermore, identify five key considerations be addressed targeting aim guiding decision making.

Language: Английский

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Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Genome Biology and Evolution, Journal Year: 2025, Volume and Issue: 17(2)

Published: Jan. 21, 2025

Ancient tooth enamel, and to some extent dentin bone, contain characteristic peptides that persist for long periods of time. In particular, from the enamel proteome (enamelome) have been used reconstruct phylogenetic relationships fossil taxa. However, enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo post mortem. This raises question as whether alone provides enough information reliable inference. We address these considerations a selection enamel-associated proteins has computationally predicted genomic data 232 primate species. created multiple sequence alignments each estimated evolutionary rate site. examined which sites overlap with parts sequences are typically isolated fossils. Based this, we simulated ancient different degrees fragmentation, followed by analysis. compared trees reference species tree. Up degree similar samples 1 2 million years ago, placements most nodes at family level consistent tested analysis combinations found composition can influence deep splits phylogeny. With our methods, provide guidance researchers how evaluate potential paleoproteomics studies before sampling valuable specimens.

Language: Английский

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Environmental DNA of aquatic macrophytes: The potential for reconstructing past and present vegetation and environments

Freshwater Biology, Journal Year: 2023, Volume and Issue: 68(11), P. 1929 - 1950

Published: July 29, 2023

Abstract Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their palaeorecord might shed light on postglacial environments. Here, we first review compare studies that use metagenomics, targeted capture, various barcoding metabarcoding markers, in order explore how each of these methods can be capture aquatic vegetation diversity change. We then investigate the extent which such a record leveraged for reconstructing local conditions, using case study based macrophyte ecological niches. find that, with state‐of‐the‐art barcode reference libraries, target P6 loop region chloroplast trn L (UAA) intron optimal maximise taxonomic resolution communities. Shotgun sequencing also retrieves high proportion diversity, but has lowest resolution, needs more widely applied before comparisons made. From our study, infer habitats sedimentary ancient records taxa. reconstructed Holocene thermal range, continentality, water pH, trophic status, conditions northern Fennoscandia. show an overall stability since 9,000 years ago, even though individual lakes display different trends variation climatic physico‐chemical conditions. Combined availability near‐exhaustive traits databases, data support wider reconstructions not limited plant inventories changes drivers. Sedimentary powerful tool measure as well lacustrine fluvial communities macrophytes.

Language: Английский

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