Genetic approaches for increasing fitness in endangered species

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(4), P. 332 - 345

Published: Jan. 10, 2022

Language: Английский

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The application gap: Genomics for biodiversity and ecosystem service management

Biological Conservation, Journal Year: 2023, Volume and Issue: 278, P. 109883 - 109883

Published: Jan. 4, 2023

The conservation of biodiversity from the genetic to community levels is fundamental for continual provision ecosystem services (ES), benefits that ecosystems provide people. Genetic and genomic diversity enhance resilience populations communities underpin functions services. We show genomics applications are mostly limited flagship species their ES management underachieved. propose a framework on how can guide sustainable bridge this genomics-ES 'application gap'. review knowledge in single (relatedness, potentially adaptive variants) or interacting (host-microorganism coevolution, hybridization) effective actions. These include population supplementation, assisted migration hybridization promote climate-adapted variants potential, control invasives, delimitation areas, provenancing strategies restoration, managing microbial function solving trade-offs. Genomics-informed actions improved outcomes supported through synergies between scientists managers at local, regional international levels, development standardized workflows, training incorporation local information. Such facilitate implementation policies such as UN 2030 goals EU Biodiversity strategy 2030, support inclusion ambitious new CBD post-2020 Global Framework hybrids.

Language: Английский

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Review of applications of artificial intelligence (AI) methods in crop research

Journal of Applied Genetics, Journal Year: 2024, Volume and Issue: 65(2), P. 225 - 240

Published: Jan. 13, 2024

Language: Английский

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Estimates of heterozygosity from single nucleotide polymorphism markers are context‐dependent and often wrong

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(4)

Published: March 3, 2024

Abstract Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it estimated single nucleotide polymorphisms (SNPs); however, has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have proposed to address these issues, our own work found them inadequate some circumstances. Here, we aimed improve the reliability comparability of estimates, specifically investigating how sample size missing data thresholds influenced calculation autosomal (heterozygosity across genome, i.e. fixed variable sites). We also explored standard practice tri‐ tetra‐allelic site exclusion could bias estimates influence eventual conclusions relating genetic diversity. Across three distinct taxa (a frog, Litoria rubella ; tree, Eucalyptus microcarpa grasshopper, Keyacris scurra ), meaningfully affected thresholds, partly due sites. These biases were inconsistent between species populations, with more diverse populations tending their severely affected, thus having potential dramatically alter interpretations propose modified framework for calculating reduces improves utility as measure diversity, whilst highlighting need existing population pipelines adjusted such sites included calculations.

Language: Английский

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Optimizing mesenchymal stem cell extracellular vesicles for chronic wound healing: Bioengineering, standardization, and safety

Regenerative Therapy, Journal Year: 2024, Volume and Issue: 26, P. 260 - 274

Published: June 1, 2024

Chronic wounds represent a significant global burden, afflicting millions with debilitating complications. Despite standard care, impaired healing persists due to factors like persistent inflammation and tissue regeneration. Mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) offer an innovative regenerative medicine approach, delivering cell-derived therapeutic cargo in engineered nanoscale delivery systems. This review examines pioneering bioengineering strategies engineer MSC-EVs into precision nanotherapeutics for chronic wounds. Emerging technologies CRISPR gene editing, microfluidic manufacturing, biomimetic systems are highlighted their potential enhance MSC-EV targeting, optimize enrichment, ensure consistent clinical-grade production. However, key hurdles remain, including batch variability, rigorous safety assessment tumorigenicity, immunogenicity, biodistribution profiling. Crucially, collaborative frameworks harmonizing regulatory science patient advocacy hold the expediting clinical translation. By overcoming these challenges, could catalyze new era of off-the-shelf therapies, restoring hope afflicted by non-healing

Language: Английский

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Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(8), P. 1893 - 1907

Published: Jan. 19, 2023

For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction individual population fitness. Despite increasing availability genomic data to measure inbreeding accurately across genome, depression studies for threatened species are still scarce due difficulty measuring fitness wild. Here, we investigate extensively monitored Tiritiri Mātangi island Aotearoa New Zealand passerine, hihi (Notiomystis cincta). First, using custom 45 k single nucleotide polymorphism (SNP) array, explore patterns by inferring homozygous segments genome. Although all have similar levels ancient inbreeding, highly inbred affected recent which probably be explained bottleneck effects such as habitat loss after European arrival their translocation 1990s. Second, on fitness, measured lifetime reproductive success, its three components, juvenile survival, adult annual survival 363 hihi. We find that global significantly affects but none remaining traits. Finally, employ genome-wide association approach test locus-specific identify 13 SNPs associated with success. Our findings suggest does impact hihi, at different scales traits, purging has therefore failed remove variants deleterious from this conservation concern.

Language: Английский

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Harnessing the omics revolution to address the global biodiversity crisis

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 80, P. 102901 - 102901

Published: Feb. 10, 2023

Language: Английский

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Challenges in quantifying genome erosion for conservation

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 26, 2022

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects population decline can lead populations into an vortex, where declining show lower genetic fitness, in turn leading to still. The fitness a due shrinking gene pool is known as erosion. Three different types erosion are highlighted this review: overall homozygosity, load runs homozygosity (ROH), which indicative inbreeding. ability quantify could be very helpful tool for conservationists, it provide them with objective, quantifiable measure use assessment species at risk extinction. link between conservation status should more apparent. Currently, no clear correlation observed current However, quantities wild populations, especially those dealing habitat fragmentation decline, may early signs deteriorating populations. Whole genome sequencing data way forward Extra screening steps hybridization included, since they potentially great impact on fitness. This way, information yielded from sequence conservationists objective method complexity quantification asks consensus bridging science its applications, remains challenging.

Language: Английский

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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

Animals, Journal Year: 2023, Volume and Issue: 13(6), P. 1089 - 1089

Published: March 18, 2023

An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type high-resolution molecular marker suitable studying diversity large numbers individuals is single nucleotide polymorphism (SNP). This review an attempt to show range applications SNPs in studies populations animals. In recent years, used analysis wild and enhanced fish invertebrate habitats, exploited migratory oceans, anadromous freshwater demersal species. identification hybrids environments, study consequences restocking conservation purposes negative effects accidentally escaping from culture. are very useful identifying genomic regions correlated with phenotypic variants relevant wildlife protection, management aquaculture. Experimental size-selective catches created tanks caused evolutionary changes life cycles fishes. The research results discussed clarify whether conditions can undergo due selective harvesting targeting fastest-growing

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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