How Can Genomics Help or Hinder Wildlife Conservation? DOI Creative Commons
Thomas L. Schmidt, Joshua A. Thia, Ary A. Hoffmann

et al.

Annual Review of Animal Biosciences, Journal Year: 2023, Volume and Issue: 12(1), P. 45 - 68

Published: Oct. 3, 2023

Genomic data are becoming increasingly affordable and easy to collect, new tools for their analysis appearing rapidly. Conservation biologists interested in using this information assist management planning but typically limited financially by the lack of genomic resources available non-model taxa. It is therefore important be aware pitfalls as well benefits applying approaches. Here, we highlight recent methods aimed at standardizing population assessments genetic variation, inbreeding, forms load that help identify past ongoing patterns interchange between populations, including those subjected disturbance. We emphasize challenges some these need adequate bioinformatic support. also consider promises approaches understand adaptive changes natural populations predict future capacity.

Language: Английский

How genomics can help biodiversity conservation DOI Creative Commons
Kathrin Theißinger, Carlos Fernandes, Giulio Formenti

et al.

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 545 - 559

Published: Feb. 16, 2023

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches applications in conservation genomics, considering practical factors, such as cost, time, prerequisite skills, current shortcomings applications. Most perform best combination with reference genomes from target species or closely related species. We review case studies to illustrate how facilitate research across tree life. conclude that time is ripe view fundamental integrate their use a practice genomics.

Language: Английский

Citations

194
Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project DOI Open Access
H. Bradley Shaffer, Erin Toffelmier,

Russ Corbett‐Detig

et al.

Journal of Heredity, Journal Year: 2022, Volume and Issue: 113(6), P. 577 - 588

Published: April 8, 2022

Abstract The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at regional scale. We describe CCGP, including all aspects project administration, collection, current progress, and future challenges. CCGP will generate, analyze, curate single high-quality reference genome 100–150 resequenced genomes for each 153 species projects (representing 235 individual species) that span ecological phylogenetic breadth California’s marine, freshwater, terrestrial ecosystems. resulting portfolio roughly 20 000 be analyzed with identical informatic genomic pipelines, providing overview hotspots within-species diversity, potential realized corridors connecting these hotspots, regions reduced diversity requiring rescue, distribution variation critical rapid climate adaptation. After 2 years concerted effort, full funding ($12M USD) has been secured, identified, funds distributed 68 laboratories 114 investigators drawn from 10 University campuses. remaining phases include completion collection analyses, delivery inferences state federal regulatory agencies help stabilize declines. aspirational goals are identify geographic long-term preservation biodiversity, prioritize those based on defensible criteria, provide foundational knowledge informs strategies both ecosystem levels.

Language: Английский

Citations

96
Plant pangenomes for crop improvement, biodiversity and evolution DOI
Mona Schreiber, Murukarthick Jayakodi, Nils Stein

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(8), P. 563 - 577

Published: Feb. 20, 2024

Language: Английский

Citations

32
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy DOI Open Access
Delphine Larivière, Linelle Abueg, Nadolina Brajuka

et al.

Nature Biotechnology, Journal Year: 2024, Volume and Issue: 42(3), P. 367 - 370

Published: Jan. 26, 2024

Language: Английский

Citations

20
Evolving spatial conservation prioritization with intraspecific genetic data DOI
Marco Andrello, Cassidy C. D’Aloia, Alicia Dalongeville

et al.

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(6), P. 553 - 564

Published: April 18, 2022

Language: Английский

Citations

45
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics DOI
Yafei Mao, Guojie Zhang

Nature Methods, Journal Year: 2022, Volume and Issue: 19(6), P. 635 - 638

Published: June 1, 2022

Language: Английский

Citations

41
The application gap: Genomics for biodiversity and ecosystem service management DOI Creative Commons
Myriam Heuertz, Sílvia B. Carvalho, Juan Galindo

et al.

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

Citations

39
Evolutionary genomics of oceanic island radiations DOI Open Access
José Cerca, Darko D. Cotoras, Vanessa C. Bieker

et al.

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 38(7), P. 631 - 642

Published: March 2, 2023

Language: Английский

Citations

36
Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories DOI Creative Commons
Blair P. Bentley, Tomás Carrasco-Valenzuela, Elisa Ramos

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(7)

Published: Feb. 7, 2023

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis the unique physiological and ecological traits enabling these species to thrive in diverse habitats remains largely unknown. Additionally, many populations have drastically declined due anthropogenic activities past two centuries, their recovery is a high global conservation priority. We generated analyzed high-quality reference genomes for leatherback ( Dermochelys coriacea ) green Chelonia mydas turtles, representing extant sea turtle families. These are highly syntenic homologous, but localized regions noncollinearity were associated with higher copy numbers immune, zinc-finger, olfactory receptor (OR) genes ORs related waterborne odorants greatly expanded turtles. Our findings suggest divergent evolution key gene families may underlie immunological sensory adaptations assisting navigation, occupancy neritic versus pelagic environments, diet specialization. Reduced collinearity was especially prevalent microchromosomes, greater content, heterozygosity, genetic distances between species, supporting critical role vertebrate evolutionary adaptation. Finally, diversity demographic histories starkly contrasted indicating had low yet stable effective population size, exhibit extremely compared other reptiles, harbor load reinforcing concern persistence under future climate scenarios. provide invaluable resources advancing our understanding best practices imperiled lineage.

Language: Английский

Citations

31
Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces DOI Creative Commons
David Peris, Emily J. Ubbelohde, Meihua Christina Kuang

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Feb. 8, 2023

Abstract Species is the fundamental unit to quantify biodiversity. In recent years, model yeast Saccharomyces cerevisiae has seen an increased number of studies related its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from same genus have been less thoroughly studied, which limited our understanding macroevolutionary events leading diversification this over last 20 million years. Here, we show geographies, hosts, substrates, phylogenetic relationships for approximately 1,800 strains, covering complete with unprecedented breadth depth. We generated analyzed genome sequences 163 strains phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic diversity within between populations, quantifies reticulation incomplete lineage sorting, demonstrates how gene flow selection affected traits, such as galactose metabolism. These findings elevate a understand biodiversity evolution in microbial eukaryotes.

Language: Английский

Citations

31