4.3 Review

New developments in the field of genomic technologies and their relevance to conservation management

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration

Carolina S. Carvalho et al.

Summary: The study introduces a comprehensive landscape genomic approach for restoring moderately disturbed and highly degraded sites, using genomic data to identify adaptive genotypes for different plant populations. The research reveals that different restoration strategies should be adopted for sites with different degradation levels, helping to define site-specific provenancing strategies for restoration initiatives.

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Summary: Augmenting gene flow is crucial for the conservation of isolated populations, but careful evaluation and monitoring are necessary. Common assessment methods may have limitations in detecting genetic rescue effects, highlighting the need for comprehensive monitoring information to improve reliability.

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Meta-analysis of genetic representativeness of plant populations under ex situ conservation in contrast to wild source populations

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Summary: The study shows that current ex situ plant collections do not effectively capture the genetic variation of wild populations. The low genetic representativeness of ex situ populations is caused by incomplete sampling from wild populations and genetic erosion during ex situ conservation. To improve the genetic representativeness of ex situ plant collections, more thorough sampling strategies in future collecting efforts and addition of new individuals where needed are necessary.

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Genetic mixing for population management: From genetic rescue to provenancing

Ary A. Hoffmann et al.

Summary: The diverse strategies for maintaining genetic diversity and adapting to changing environments in animal and plant species are essential for conservation efforts. Interventions involving deliberate movement of genotypes to enhance gene flow are gaining interest, with potential applications at different scales. Understanding mechanisms behind species decline and community impact is crucial for successful implementation of these strategies, with a need to consider risks and trade-offs.

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Genetic consequences of long-term small effective population size in the critically endangered pygmy hog

Langqing Liu et al.

Summary: Human disturbance and climate change have a negative impact on habitat integrity and size, leading to population decline and habitat fragmentation for wild fauna and flora. Analysis of the genomic data of the pygmy hog reveals a very small historical population size with no recent inbreeding, but evidence of harmful mutation accumulation exceeding purifying selection. Care must be taken in conservation efforts to prevent further inbreeding depression and mitigate potential environmental changes.

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Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild

Pratibha Baveja et al.

Summary: By utilizing historical DNA, the study identified three deeply diverged lineages within the Asian Pied Starling complex, providing insights for commencing a dedicated ex situ breeding program for the extinct-in-the-wild Javan Pied Starling. The research also serves as a blueprint for addressing similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.

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Harnessing landscape genomics to identify future climate resilient genotypes in a desert annual

Daniel F. Shryock et al.

Summary: Local adaptation plays a critical role in shaping species responses to changing environments, highlighting the importance of using seeds with favorable adaptations to predict and promote long-term resilience in the face of rapid climate change. Landscape genomics is identified as a cost-efficient approach for identifying future-adapted genotypes, with the study demonstrating the use of genome scans to identify potentially adaptive loci related to climate and vegetation metrics. By integrating species distribution models and causal modeling, the study provides insights into how temperature and precipitation influence spatial turnover in adaptive loci, suggesting warm-adapted genotypes may expand their climate niche by midcentury to cope with future climates. Prioritizing seed collection efforts on genotypes with expanding future habitat represents a promising strategy for restoration practitioners to address rapidly changing climates.

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The importance of genomic variation for biodiversity, ecosystems and people

Madlen Stange et al.

Summary: The 2019 United Nations Global Assessment Report on Biodiversity and Ecosystem Services estimated that approximately 1 million species are at risk of extinction. Genetics and genomics research can contribute to understanding the adaptive potential of species and communities, ultimately improving the conditions of ecosystems and people.

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High genomic diversity maintained by populations of Carex scirpoidea subsp. convoluta, a paraphyletic Great Lakes ecotype

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Summary: Range-limited endemic taxa are threatened by loss of genomic diversity, but dioecy and a nearly obligate outcrossing mode of reproduction may help maintain genomic diversity in these taxa. Phylogenomic and Bayesian analyses suggest that locally adapted ecotypes may exist within these taxa, originating from periglacial refugia south of the Laurentide Ice Sheet. Efforts should focus on habitat protection and replanting for habitat restoration to aid in conservation of these populations.

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Summary: The study focused on the restoration of the extinct Adriatic Beluga sturgeon population, providing informed criteria for reintroduction in Italian rivers. Genetic analysis revealed significant genetic differentiation between the Black-Azov and Caspian basins, indicating past isolated populations and deep paleogeographical changes in the areas.

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Summary: Biodiversity is threatened globally, and population genomics has emerged as a valuable tool for wildlife conservation. By providing precise estimates of population features and identifying genetic variants, genomics can help assess populations' ability to adapt to environmental changes and enhance conservation efforts.

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Integrating biobanking minimises inbreeding and produces significant cost benefits for a threatened frog captive breeding programme

Lachlan G. Howell et al.

Summary: Captive breeding is an important part of global conservation efforts, but integrating biobanking of founder sperm can greatly reduce costs and achieve long-term genetic diversity retention targets. By using frozen sperm for backcrossing, the study showed significant reductions in expenditure and the potential for producing more animals of higher genetic quality through assisted breeding. This innovation could enhance credibility and support for captive breeding as a conservation strategy.

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Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression

Christopher C. Kyriazis et al.

Summary: Human-driven habitat fragmentation and loss have resulted in small and isolated plant and animal populations facing high risk of extinction, mainly due to inbreeding depression. While the traditional approach for managing these populations involves maintaining high genetic diversity, recent research suggests that minimizing strongly deleterious variation may be more important in reducing extinction risk.

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Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive

Kevin P. Oh et al.

Summary: Research has found significant genetic variations in invasive mouse populations colonizing islands, with moderate to high levels of differentiation from nearby source populations. Locally fixed Cas9 genomic targets were observed in female fertility genes across all island populations.

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Population structure, inbreeding and admixture in local cattle populations managed by community-based breeding programs in Burkina Faso

Dominique Ouedraogo et al.

Summary: High-throughput genomic markers provide insights into genetic diversity, inbreeding, and introgression in livestock breeding programs, especially in developing countries like West Africa. The study analyzed key population parameters in three neighboring populations in Burkina Faso, revealing moderate levels of inbreeding and concerns about crossbreeding levels in presumably pure African taurine cattle. Future rounds of bull selection in the breeding program will utilize genomic information about admixture levels to improve management practices.

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An ethical analysis of cloning for genetic rescue: Case study of the black-footed ferret

Ronald L. Sandler et al.

Summary: Genetic rescue is a tool for managing genetic load and enhancing fitness by introducing unique genomes into populations. Biobanks provide a potential source of cryopreserved material, such as fibroblasts, which may require cloning. Ethical analysis is essential to determine the justification for cloning and address related issues responsibly. An ethical framework is provided for conservation cloning, with a case study on using cloning for genetic rescue in black-footed ferret recovery efforts.

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Genome-wide diversity in the California condor tracks its prehistoric abundance and decline

Jacqueline A. Robinson et al.

Summary: The study focused on the genome of the California condor, Andean condor, and turkey vulture, revealing that the California condor genome retains a high degree of variation due to its historically high abundance. Correlations between genome-wide diversity and recombination rate suggest a history of purifying selection against linked deleterious alleles, providing a promising foundation for future restoration efforts.

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Spatial areas of genotype probability: Predicting the spatial distribution of adaptive genetic variants under future climatic conditions

Estelle Rochat et al.

Summary: In the context of rapid global change, the SPAG method provides a flexible approach to combine loci under different types of intergenic relationships and assess evolutionary potential predictions. By integrating with climate change projections, the method can forecast the future spatial distribution of genotypes and identify vulnerable populations lacking adaptive genotypes. The SPAG methodology is an efficient and flexible tool to characterize evolutionary potential across landscapes and transpose evolutionary information into conservation frameworks.

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Genetic diversity and selection signatures in maize landraces compared across 50 years of in situ and ex situ conservation

Francis Denisse McLean-Rodriguez et al.

Summary: Genomics-based longitudinal comparisons between ex situ and in situ agrobiodiversity conservation strategies reveal that genome-wide diversity is similar, with in situ samples showing fewer SNPs and lower genetic distances. Additionally, loci under selection in in situ conservation were identified, potentially linked to farmer selection criteria.

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An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes

Yann X. C. Bourgeois et al.

Summary: The continuous improvement of high-throughput sequencing techniques has enabled the production of whole genome data in various species, which in turn provides better tools for integrating selection into historical frameworks. However, the plethora of analytical tools may confuse users and hinder the dissemination of the latest methods.

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Genomic and fitness consequences of inbreeding in an endangered carnivore

Malin Hasselgren et al.

Summary: The study revealed higher genetic diversity in immigrant descendants compared to natives, but the genetic rescue effect did not persist through subsequent generations. Additionally, foxes with lower levels of inbreeding had a higher likelihood of surviving to one year of age.

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Integrating genomics in population models to forecast translocation success

Travis Seaborn et al.

Summary: Whole-genome sequencing is changing the way we understand organismal biology and can inform population dynamics, but there is still much to learn about how genomic differences impact population dynamics in the real world. By using genomics and genetics data to inform organismal performance, we can better understand the drivers of population dynamics and improve translocation success through the development and validation of forecasting models. Integrating lab-based and field-collected data with model-driven research can help address challenges in restoration ecology and aid in the translocation of locally adapted genotypes.

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Resilience in Greenland intertidal Mytilus: The hidden stress defense

Melody S. Clark et al.

Summary: The Arctic is warming rapidly, allowing invasive species to survive. Some marine species can tolerate high temperatures, but the Mytilus edulis is usually unable to survive in extreme heat. Research indicates that M. edulis has a wide acclimation ability, enabling it to withstand Arctic warming and temperature variations.

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Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations

Johanna von Seth et al.

Summary: Highly endangered species like the Sumatran rhinoceros are facing threats from inbreeding which could lead to higher risk of extinction for small, isolated populations. The presence of genetic burden and inbreeding in rhinoceros populations suggest that assisted gene flow among different populations may be needed in the future to reduce the risk of inbreeding depression.

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Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Sean Hoban et al.

Summary: Global conservation policies have historically overlooked the importance of protecting and monitoring genetic diversity, which is crucial for species adaptation, ecosystem resilience, and societal innovation. Recent advancements in knowledge, technology, and capacity now offer the possibility for integrating genetic diversity more effectively into policy instruments and conservation efforts, ultimately enhancing the effectiveness of biodiversity conservation.

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Climate change impact on cultivated and wild cacao in Peru and the search of climate change-tolerant genotypes

Viviana Ceccarelli et al.

Summary: The study found that different modelling approaches are required for cultivated and wild cacao, and spatial filtering resolution has a significant impact on future suitability predictions. Overall, the models predict a contraction of suitable area for cultivated cacao while a more positive future for wild cacao in Peru. Changes in ecogeographical zones are expected in 8%-16% of the distribution, and several potential areas for climate change-tolerant genotypes were identified.

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Expected demographic and genetic declines not found in most zoo and aquarium populations

Judy Che-Castaldo et al.

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Henry L. North et al.

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First evidence of deviation from Mendelian proportions in a conservation programme

Catherine E. Grueber et al.

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