Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods DOI Creative Commons
William A Marsh, Andie Hall, Ian Barnes

et al.

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

Published: Feb. 19, 2025

Abstract While DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way sourcing taxonomically validated for is to use museum collections. However, degradation intrinsic historical specimens can, if not addressed wet lab, lead low quality data generation and severely limit scientific output. Several extraction library build that designed work with degraded have been developed, although ability implement these at scale cost has yet be formally addressed. Here, performance widely used compared using specimens. We find while our selected do significantly differ yield, Santa Cruz Reaction (SCR) method only most effective retrieving from but also easily implemented high throughput cost. Results highlight importance lab protocol on yield. An optimised “sample sequencing” high-throughput which incorporates SCR included allow easy uptake by wider community.

Language: Английский

Population genomics for wildlife conservation and management DOI
Paul A. Hohenlohe, W. Chris Funk,

Om P. Rajora

et al.

Molecular Ecology, Journal Year: 2020, Volume and Issue: 30(1), P. 62 - 82

Published: Nov. 4, 2020

Biodiversity is under threat worldwide. Over the past decade, field of population genomics has developed across nonmodel organisms, and results this research have begun to be applied in conservation management wildlife species. Genomics tools can provide precise estimates basic features populations, such as effective size, inbreeding, demographic history structure, that are critical for efforts. Moreover, studies identify particular genetic loci variants responsible inbreeding depression or adaptation changing environments, allowing efforts estimate capacity populations evolve adapt response environmental change manage adaptive variation. While connections from been slow develop, these increasingly strengthening. Here we review primary areas which approaches management, highlight examples how they used, recommendations building on progress made field.

Language: Английский

Citations

477
The era of reference genomes in conservation genomics DOI Creative Commons
Giulio Formenti, Kathrin Theißinger, Carlos Fernandes

et al.

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(3), P. 197 - 202

Published: Jan. 24, 2022

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate genomes representing global biodiversity. These provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses population functional genomics, are expected revolutionize conservation genomics.

Language: Английский

Citations

235
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
Opportunities and challenges of macrogenetic studies DOI
Deborah M. Leigh, Charles B. van Rees, Katie L. Millette

et al.

Nature Reviews Genetics, Journal Year: 2021, Volume and Issue: 22(12), P. 791 - 807

Published: Aug. 18, 2021

Language: Английский

Citations

109
Threatened Species Initiative: Empowering conservation action using genomic resources DOI Creative Commons
Carolyn J. Hogg, Kym Ottewell,

Peter Latch

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(4)

Published: Jan. 18, 2022

Globally, 15,521 animal species are listed as threatened by the International Union for Conservation of Nature, and these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives developing resources, yet production a reference alone does not conserve species. The allows us to develop suite tools understand both genome-wide functional diversity within between practitioners use their decision-making. But, at present there is an implementation gap release information data in applied practitioners. In May 2020, we launched Threatened Species Initiative brought consortium biologists, population bioinformaticians, geneticists, ecologists together with agencies across Australia, including government, zoos, nongovernment organizations. Our objective create foundation advance our understanding key Australian species, ultimately empower access apply decision-making processes through web-based portal. Currently, 61 from range taxa, more 130 collaborators academia, Developed direct consultation government threatened-species managers other practitioners, herein framework meeting needs systematic approach integrating genomics into recovery.

Language: Английский

Citations

77
The contribution of historical processes to contemporary extinction risk in placental mammals DOI
Aryn P. Wilder, Megan A. Supple, Ayshwarya Subramanian

et al.

Science, Journal Year: 2023, Volume and Issue: 380(6643)

Published: April 27, 2023

Species persistence can be influenced by the amount, type, and distribution of diversity across genome, suggesting a potential relationship between historical demography resilience. In this study, we surveyed genetic variation single genomes 240 mammals that compose Zoonomia alignment to evaluate how effective population size (

Language: Английский

Citations

60
Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life DOI Creative Commons
Ann M. Mc Cartney, Jane Anderson, Libby Liggins

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(4)

Published: Jan. 18, 2022

The field of genomics has benefited greatly from its “openness” approach to data sharing. However, with the increasing volume sequence information being created and stored growing number international efforts, equity openness is under question. United Nations Convention Biodiversity aims develop adopt a standard policy on access benefit-sharing for across signatory parties. This standardization will have profound implications research, requiring new definition open redefinition not unwarranted, as limitations unintentionally introduced barriers engagement some, including Indigenous Peoples. commentary provides an insight into key challenges faced by researchers who aspire protect conserve global biodiversity, flora fauna, presents immediate, practical solutions that, if implemented, equip community both diversity inclusivity required respectfully biodiversity.

Language: Английский

Citations

64
Reference genomes for conservation DOI

Sadye Paez,

R.H. Kraus, Beth Shapiro

et al.

Science, Journal Year: 2022, Volume and Issue: 377(6604), P. 364 - 366

Published: July 21, 2022

High-quality reference genomes for non-model species can benefit conservation.

Language: Английский

Citations

63
The phenotypic costs of captivity DOI Creative Commons
Ross Crates, Dejan Stojanović, Robert Heinsohn

et al.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2022, Volume and Issue: 98(2), P. 434 - 449

Published: Nov. 7, 2022

The breeding of threatened species in captivity for release is a central tool conservation biology. Given gloomy predictions biodiversity trends the Anthropocene, captive will play an increasingly important role preventing future extinctions. Relative to wild, environments drastically alter selection pressures on animals. Phenotypic change animals response these altered can incur fitness costs post-release, jeopardising their potential contribution population recovery. We explore ways which hinder expression wild phenotypes. also stress that phenotypes captive-bred differ from counterparts multiple remain poorly understood. propose five new research questions relating impact reintroduction With better use monitoring and experimental reintroductions, more robust evidence base should help inform adaptive management minimise phenotypic captivity, improving success animal reintroductions.

Language: Английский

Citations

54
Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates DOI Creative Commons

Paige Matheson,

Angela McGaughran

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Aug. 17, 2022

Abstract Biological invasions drive environmental change, potentially threatening native biodiversity, human health, and global economies. Population genomics is an increasingly popular tool in invasion biology, improving accuracy providing new insights into the genetic factors that underpin success compared to research based on a small number of loci. We examine extent which population genomic resources, including reference genomes, have been used or are available for invasive species research. find 82% International Union Conservation Nature “100 Worst Invasive Alien Species” list studied using some form data, but just 32% these data. Further, 55% list’s lack genome. With incursion rates escalating globally, understanding how genome-driven processes facilitate critical, despite promising trend increasing uptake, “invasion genomics” still its infancy. discuss data can enhance our biological inform proactive detection management species, we call more specifically targets this area.

Language: Английский

Citations

39