Cooling perspectives on the risk of pathogenic viruses from thawing permafrost

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

ABSTRACT Climate change is inducing wide-scale permafrost thaw in the Arctic and subarctic, triggering concerns that long-dormant pathogens could reemerge from thawing ground initiate epidemics or pandemics. Viruses, as opposed to bacterial pathogens, garner particular interest because outbreaks cannot be controlled with antibiotics, though effects can mitigated by vaccines newer antiviral drugs. To evaluate potential hazards posed viral emerging permafrost, we review information a diverse range of disciplines. This includes efforts recover infectious virus human remains, studies on disease occurrence polar animal populations, investigations into persistence infectivity assessments exposure enormous diversity present environment. Based currently available knowledge, conclude risk viruses no greater than other environments such temperate soils aquatic systems.

Language: Английский

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Unraveling the diversity and cultural heritage of fruit crops through paleogenomics

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(5), P. 398 - 409

Published: Feb. 28, 2024

Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which being replaced a limited set high-yielding ones. This article delves into potential paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, tomatoes, recent studies showcase effectiveness paleogenomic techniques in identifying understanding genetic traits crucial for crop resilience, disease resistance, nutritional value. The approach not only tracks landrace dispersal introgression but also sheds light domestication events. In face major future environmental challenges, integrating with modern breeding strategies emerges as promising avenue significantly bolster sustainability.

Language: Английский

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From genomic threat assessment to conservation action

Cell, Journal Year: 2024, Volume and Issue: 187(5), P. 1038 - 1041

Published: Feb. 1, 2024

Genomic approaches have the potential to play a pivotal role in conservation, both detect threats species and populations restore biodiversity through actions. We here separate these into two subdisciplines, vulnerability restoration genomics, discuss current applications, outstanding questions, future potential. At its core, conservation genomics seeks leverage power of genomic technologies address questions regarding genetic diversity, adaptation, resilience endangered threatened organisms.1Ryder O.A. Conservation genomics: applying whole genome studies efforts.Cytogenet. Genome Res. 2005; 108: 6-15Crossref PubMed Scopus (0) Google Scholar Moreover, aim is typically that by addressing we can aid restoring viability species. Since advent high-throughput sequencing technologies, field has emerged as frontier discipline pursuit quantify mitigate crisis across kingdoms life.2Segelbacher G. Bosse M. Burger P. Galbusera Godoy J.A. Helsen Hvilsom C. Iacolina L. Kahric A. Manfrin et al.New developments their relevance management.Conserv. Genet. 2022; 23: 217-242Crossref (27) make it possible identify nearly all variation within individuals populations, allowing for assessments genome-wide diversity direct measures inbreeding coefficients. With ever-improving annotations inference methods, also possess ability those mutations cause regulatory or protein-coding changes, estimate putative effect on fitness, subsequently obtain insights load. The majority investigations concerning concentrated discerning and, some extent, quantifying factors contribute population declines loss, research focus term "vulnerability genomics." However, from management perspective, developing concrete actions aimed at viability, refer "restoration These subdisciplines are closely intertwined, species, ecosystems vulnerable essential thus ensuring survival (Figure 1). In past decades, broad array identified intrinsic processes such inbreeding-driven expression recessive deleterious alleles, accumulation load drift, well outbreeding depression, i.e., reduction individual fitness due crosses between differentially adapted populations. helped managers policymakers better understand whether pose threat several cases led changes policies. For example, revealed Scandinavian wolves suffer depression,3Kardos Åkesson Fountain T. Flagstad Ø. Liberg O. Olason Sand H. Wabakken Wikenros Ellegren consequences intensive an isolated wolf population.Nat. Ecol. Evol. 2018; 2: 124-131https://doi.org/10.1038/s41559-017-0375-4Crossref (116) which prompted Swedish government adopt policy reducing protecting Finnish/Russian immigrant during yearly license hunt. data been used reveal differences fragmented shed light impacts habitat destruction fragmentation. addition, allow identification markers associated with pollutant exposure thereby help measure susceptibility different pollution.4Hawkins N.J. Bass Dixon Neve evolutionary origins pesticide resistance.Biol. Rev. Camb. Philos. Soc. 2019; 94: 135-155Crossref (341) cases, may develop adaptations cope certain pollutants. adaptive potentially offering how evolve response environmental stressors. inclusion DNA obtained historical samples allowed quantification temporal inbreeding, mutational load5Díez-Del-Molino D. Sánchez-Barreiro F. Barnes I. Gilbert M.T.P. Dalén Quantifying Temporal Erosion Endangered Species.Trends 33: 176-185Abstract Full Text PDF (97) leveraged recent fragmentation losses connectivity demonstrating reduced levels gene flow time. deeper timescale, paleogenomic span one glacial cycles examine demographic climatic changes.6Dalén Heintzman P.D. Kapp J.D. Shapiro B. Deep-time paleogenomics limits survival.Science. 2023; 382: 48-53Crossref Such provide valuable extent sensitive climate change, be incorporated modeling under change scenarios. uncover previously unrecognized distinct lineages, helping instances where escaped our radar, status important units were unknown.7Nater Mattle-Greminger M.P. Nurcahyo Nowak M.G. de Manuel Desai Groves Pybus Sonay T.B. Roos al.Morphometric, Behavioral, Evidence New Orangutan Species.Curr. Biol. 2017; 27: 3576-3577Abstract DNA-based methods poaching hotspots building reference databases establish connections variants geographical locations. then pinpoint origin wildlife products, areas most prevalent, tracing products various stages supply chain. Furthermore, tools proven instrumental identifying species-associated microorganisms, vital assess pathogen threats, co-evolution, local adaptation microbiome, monitoring foraging habits.8Carthey A.J.R. Blumstein D.T. Gallagher R.V. Tetu S.G. Gillings M.R. Conserving holobiont.Funct. 2020; 34: 764-776Crossref (28) Finally, analysis provides effective means non-invasive observations distributions, migration patterns, structure Genomics indispensable providing solutions targeted are, instance, being enhance effectiveness captive breeding programs. Unraveling relatedness among guide selective strategies, optimizing facilitating recovery long-term persistence.2Segelbacher applications applied detecting counteracting hybridization related taxa, including preventing admixture domesticates wild conspecific This not only preserving integrity but helpful programs management, efforts focused unadmixed populations.9Frandsen Fontsere Nielsen S.V. Hanghøj K. Castejon-Fernandez N. Lizano E. Hughes Hernandez-Rodriguez J. Korneliussen T.S. Carlsen al.Targeted genetics chimpanzee.Heredity. 125: 15-27Crossref (10) Comparable techniques rewilding projects, information suitable release considering presence and/or variants. realm making substantial contributions international combating illegal trade. precise identification, crucial when dealing derived flora, ivory, fur, medicines prosecution poachers smugglers improve toward dismantling illicit trade networks.10Wasser S.K. Wolock C.J. Kuhner M.K. Brown 3rd, J.E. Morris Horwitz R.J. Wong Fernandez Otiende M.Y. Hoareau Y. al.Elephant genotypes size transnational ivory traffickers.Nat. Hum. Behav. 6: 371-382Crossref (11) enhanced identify, track, impact invasive diseases, serving potent instrument examining spillover transmissions species.11Scheele B.C. Pasmans Skerratt L.F. Berger Martel Beukema W. Acevedo A.A. Burrowes P.A. Carvalho Catenazzi al.Amphibian fungal panzootic causes catastrophic ongoing loss biodiversity.Science. 363: 1459-1463Crossref (714) directly ensure disease-carrying geographic regions high disease prevalence other additionally comprehension reproductive biology, unlocking insights, artificial insemination applied. obtaining sequence aids tool gauging sustainability reintroduction initiatives, refining strategies advancing native ecosystems. stream water has, monitor distribution re-introduced fish Germany.12Riaz Kuemmerlen Wittwer Cocchiararo Khaliq Pfenninger Combining evaluate success freshwater fish.Ecol. Appl. 30e02034Crossref (16) science now entered era unprecedented achieving resolutions once considered unattainable. Nonetheless, find ourselves framework yet fully translate vulnerabilities quantified relative threats. To accurately variety key unknowns remain outstanding. Identifying individual's importance purposes, translation computational variant predictions based models real-world remains highly uncertain. there lack component adaptive, instead, rely summary statistics proxy variation. while multitude load, suggestive types analyses demonstrate link estimates let alone specific causative lead success. date, mostly relies estimating using translation, frameshift stop codon variants.13Dussex Morales H.E. Grossen van Oosterhout Purging conservation.Trends 38: 961-969Abstract (7) Novel machine-learning approaches, capable 3D protein structure, broader contexts variants, could new avenues enhancing accuracy estimates. given limited attention structural adaptability, primarily challenges short read data. Ongoing improvements affordability long-read platforms will understanding persistence still characterize seem neutral today future. Additionally, interact each other, improved Can context beneficial combined another elsewhere genome, do interactions? Innovative frameworks employing holistic biological pathway along pathways, theory integrate interplay improving constraints become essential. Could novel variant, introduced via translocation engineering, confers short-term advantages, impede evolution genes, locking pathways optimum? Related this interaction informing planning translocations. Are locally adapted, even if they numerous mutations, more fit than non-locally fewer mutations? assessment effects resulting involves target, followed evaluation recognized phenotypic disrupting gene, conducted model It clear what extrapolate If harmful likely detrimental species? foresee deciphering functions microbes microbiome increasingly studies.8Carthey Which resilience, presence-absence influence whole? anticipate significant development advanced extraction portable capture probes, cell sorting, single-cell analysis, low-input protocols. Combined increasing internet connectivity, capability generate subsequent cloud-based bioinformatic low-quality, cost-effective scale revolutionize immediate widespread application field. As increases, expect part conservation. open opportunities, selecting optimal (e.g., assisted species) managing reproduction minimize risk introducing diseases artificially select against strongly carry entirely fixed engineering CRISPR-Cas9, biobanked lines re-introduce wild-type back population. alleles further informed pre-bottleneck specimens held natural history collections.14Cowl V.B. Comizzoli Appeltant R. Bolton R.L. Browne Holt W.V. Penfold L.M. Swegen Walker S.L. Williams S.A. Cloning Twenty-First Century Its Place Species Conservation.Annu. Anim. Biosci. 12https://doi.org/10.1146/annurev-animal-071423-093523Crossref While early stage, enable resurrection lost extinct ecosystem functions. reintroduce places extinct, considerable use eDNA localities comprise habitats. would involve detection exotic predators competitors assessing eradication efforts), pathogens verifying food sources mutualistic exist. costs processing continues decline, establishment comprehensive becoming feasible. advancement holds great promise poaching. By law enforcement agencies detailed maps, real-time field, confiscated trafficked animals achieved rapidly, bolstering capacities fight investigation affect resistance survival, susceptible infectious diseases.15Damas G.M. Keough K.C. Painter C.A. Persky N.S. Corbo Hiller Koepfli K.-P. Pfenning A.R. Zhao al.Broad host range SARS-CoV-2 predicted comparative ACE2 vertebrates.Proc. Natl. Acad. Sci. USA. 117: 22311-22322Crossref (361) knowledge animal vaccination initiatives implementation isolation Ultimately, unlock full tool, genomics-based need describe face use. envision former pressing latter them Importantly, implemented, additional further. T.v.d.V. acknowledges support SciLifeLab & Wallenberg Data Driven Life Science Program (KAW 2020.0239). L.D. Research Council (2021-00625) European Union (ERC, PrimiGenomes, 101054984). member scientific advisory board Colossal Biosciences. Five decades al.CellFebruary 29, 2024In BriefSome discoveries life sciences over last 50 years stem genomics. seen large-scale collaborative yield fundamental milestones results, Human Project. Despite long road ahead, progress basic clinical drives sweeping cure complex human ailments blood psychiatric disorders, metabolic cancer, neurodegeneration. large tent-pole endeavors receive attention, cutting-edge modern foundational happens daily biomedical sciences. Full-Text

Language: Английский

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Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

ABSTRACT The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human‐impacted oceans. Sequencing sedimentary DNA (sedaDNA) is an emerging method generating high‐resolution time‐series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun‐metagenomics, it remains unclear if these methodological differences affect diversity metrics. We compared methods using from archived sediment record sampled Skagerrak, North Sea, spanning almost 8000 years. performed a eukaryotic 18S rRNA region (V9) sequenced 153–229 million metagenomic reads per sample. Our results show limited overlap between metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, detections became inconsistent samples older than 2000 years, while metagenomics taxa throughout time series. observed divergent patterns alpha diversity, indicating decreased richness towards present showing increase. beta were similar methods, discrepancies data comparisons. findings demonstrate that choice significantly impacts record. While we stress variation degradation among may not be strongly affected, researchers should exonerate explanations cores, particularly when considering before making ecological interpretations.

Language: Английский

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Paleobiogeographic insights gained from ecological niche models: progress and continued challenges

Paleobiology, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 21

Published: March 11, 2025

Abstract The spatial distribution of individuals within ecological assemblages and their associated traits behaviors are key determinants ecosystem structure function. Consequently, determining the species, how distributions influence patterns species richness across ecosystems today in past, helps us understand what factors act as fundamental controls on biodiversity. Here, we explore niche modeling has contributed to understanding spatiotemporal past biodiversity evolutionary processes. We first perform a semiquantitative literature review capture studies that applied models (ENMs) identifying 668 studies. coded each study according focal taxonomic group, whether used fossil evidence, it relied evidence or methods addition ENMs, scale study, temporal intervals included ENMs. trends publication categories anchor discussion recent technical advances modeling, focusing paleobiogeographic ENM applications. then explored contributions ENMs paleobiogeography, with particular focus examining drivers range dynamics; phylogeography within-lineage macroevolutionary processes, including change, speciation, extinction; community assembly; conservation paleobiogeography. Overall, powerful tools for elucidating patterns. most commonly Quaternary dynamics, but an increasing number use gain important insight into both processes pre-Quaternary times. Deeper integration phylogenies may further extend those insights.

Language: Английский

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Genomics of Wild Relatives of Fruit Trees and Its Application in Future Breeding Programs

Published: Jan. 1, 2025

Language: Английский

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Museomics and morphological analyses of historical and contemporary peninsular Italian wolf (Canis lupus italicus) samples

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 4, 2025

Abstract After centuries of decline and protracted bottlenecks, the peninsular Italian wolf population has naturally recovered. However, an exhaustive comprehension effects such a conservation success is still limited by reduced availability historical data. Therefore, in this study, we morphologically genetically analyzed contemporary samples, also exploiting optimization innovative bone DNA extraction method, to describe morphological variability subspecies its genetic diversity during last 30 years. We obtained high amplification genotyping rates for tissue, blood petrous samples. Multivariate, clustering analyses confirmed that Apennine well-distinguishable from both European wolves dogs, with no natural immigration other populations, while remained low across three decades, without significant changes between specimens. This study highlights scientific value well-maintained museum collections, demonstrates bones represent reliable sources, emphasizes need long-term monitor dynamics peculiar populations ensure appropriate management actions.

Language: Английский

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A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT Large‐scale DNA screening of palaeontological and archaeological collections remains a limiting costly factor for ancient studies. Several extraction protocols are routinely used in laboratories have even been automated on robotic platforms. Robots offer solution high‐throughput but the costs, as well necessity trained technicians engineers, can be prohibitive some laboratories. Here, we present alternative to robot‐based using 96‐column plate. When compared routine single MinElute columns, retrieved highly similar endogenous contents, an important metric screening. Mitogenomes with coverage depth greater than 0.1× could generated allowed taxonomic assignment. However, average fragment lengths, damage library complexities significantly differed between methods these differences became nonsignificant after modification our purification protocol. Our method allows generation 96 extracts within approximately 4 hours laboratory work while bringing cost down by ~39% columns. Additionally, formally demonstrate that addition Tween‐20 during elution step results higher complexity libraries, thereby enabling genome same sequencing effort.

Language: Английский

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Use and dual use of synthetic biology

Comptes Rendus Biologies, Journal Year: 2025, Volume and Issue: 348(G1), P. 71 - 88

Published: March 7, 2025

Language: Английский

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Palaeogenomic inference of biodiversity dynamics across Quaternary timescales

Published: March 18, 2025

Language: Английский

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