Genomic Diversity as a Key Conservation Criterion: Proof‐of‐Concept From Mammalian Whole‐Genome Resequencing Data DOI Creative Commons
Jong Yoon Jeon, Andrew N. Black, Erangi J. Heenkenda

и другие.

Evolutionary Applications, Год журнала: 2024, Номер 17(9)

Опубликована: Сен. 1, 2024

ABSTRACT Many international, national, state, and local organizations prioritize the ranking of threatened endangered species to help direct conservation efforts. For example, International Union for Conservation Nature (IUCN) assesses Green Status publishes influential Red List species. Unfortunately, such yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, future potential. To test whether populations genome sequences could improve assessments, we estimated metrics from 82 publicly available mammalian datasets examined their statistical association attributes related conservation. We also considered intrinsic biological factors, including trophic level body mass, that impact quantified relative influences. Our results identify key population are both reflective predictive IUCN categories. Specifically, our analyses revealed Watterson's theta (the mutation rate) autozygosity (a product inbreeding) current categorization, likely because demographic declines lead “listing” decisions reduce levels standing variation. argue by virtue this relationship, like leverage emerging sequence data categorize threat rankings (especially in otherwise data‐deficient species) and/or enhance assessments establish a baseline monitoring. Thus, paper (1) outlines theoretical empirical justification new GD‐based assessment criterion, (2) provides bioinformatic pipeline estimating data, (3) suggests an analytical framework can be used measure while providing quantitative context consideration authorities.

Язык: Английский

The crucial role of genome-wide genetic variation in conservation DOI
Marty Kardos, Ellie E. Armstrong, Sarah W. Fitzpatrick

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(48)

Опубликована: Ноя. 12, 2021

The unprecedented rate of extinction calls for efficient use genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field conservation biology has placed too much focus on conserving genome-wide genetic variation, should instead managing subset functional variation is thought affect fitness. Here, we critically evaluate feasibility likely benefits this approach in conservation. We find population theory empirical results show generally best prevent inbreeding depression loss adaptive potential from driving populations toward extinction. Focusing efforts presumably will only be feasible occasionally, often misleading, counterproductive when prioritized over variation. Given increasing habitat other environmental changes, failure recognize detrimental effects lost long-term viability worsen biodiversity crisis.

Язык: Английский

Процитировано

356
Genetic load: genomic estimates and applications in non-model animals DOI
Giorgio Bertorelle, Francesca Raffini, Mirte Bosse

и другие.

Nature Reviews Genetics, Год журнала: 2022, Номер 23(8), С. 492 - 503

Опубликована: Фев. 8, 2022

Язык: Английский

Процитировано

191
Deleterious Variation in Natural Populations and Implications for Conservation Genetics DOI Creative Commons
Jacqueline A. Robinson, Christopher C. Kyriazis, Stella Yuan

и другие.

Annual Review of Animal Biosciences, Год журнала: 2022, Номер 11(1), С. 93 - 114

Опубликована: Ноя. 4, 2022

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest elucidating the impact deleterious variation on extinction risk optimizing management strategies accounting for such mutations. Quantifying understanding effects population history complex endeavors because we do not know strength selection acting each mutation. Further, effect demographic depends against mutation degree dominance. Here clarify how can be quantified studied natural populations. We then discuss different factors, as small size, nonequilibrium size changes, inbreeding, gene flow, affect variation. Lastly, provide guidance studying nonmodel populations conservation concern.

Язык: Английский

Процитировано

90
Inbreeding depression explains killer whale population dynamics DOI
Marty Kardos, Yaolei Zhang, Kim M. Parsons

и другие.

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(5), С. 675 - 686

Опубликована: Март 20, 2023

Язык: Английский

Процитировано

85
Purging and accumulation of genetic load in conservation DOI Creative Commons
Nicolás Dussex, Hernán E. Morales, Christine Grossen

и другие.

Trends in Ecology & Evolution, Год журнала: 2023, Номер 38(10), С. 961 - 969

Опубликована: Июнь 19, 2023

Our ability to assess the threat posed by genetic load small and declining populations has been greatly improved advances in genome sequencing computational approaches. Yet, considerable confusion remains around definitions of its dynamics, how they impact individual fitness population viability. We illustrate both selective purging drift affect distribution deleterious mutations during size decline recovery. show this impacts composition load, affects extinction risk recovery potential populations. propose a framework examine dynamics advocate for introduction estimates management endangered

Язык: Английский

Процитировано

79
The contribution of historical processes to contemporary extinction risk in placental mammals DOI
Aryn P. Wilder, Megan A. Supple, Ayshwarya Subramanian

и другие.

Science, Год журнала: 2023, Номер 380(6643)

Опубликована: Апрель 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 (

Язык: Английский

Процитировано

61
Key issues in assessing threats to sea turtles: knowledge gaps and future directions DOI Creative Commons
Mariana M. P. B. Fuentes,

Erin McMichael,

Connie Y. Kot

и другие.

Endangered Species Research, Год журнала: 2023, Номер 52, С. 303 - 341

Опубликована: Сен. 20, 2023

Sea turtles are an iconic group of marine megafauna that have been exposed to multiple anthropogenic threats across their different life stages, especially in the past decades. This has resulted population declines, and consequently many sea turtle populations now classified as threatened or endangered globally. Although some worldwide showing early signs recovery, still face fundamental threats. is problematic since important ecological roles. To encourage informed conservation planning direct future research, we surveyed experts identify key contemporary (climate change, take, fisheries, pollution, disease, predation, coastal development) faced by turtles. Using survey results current literature, also outline knowledge gaps our understanding impact these how targeted often involving emerging technologies, could close those gaps.

Язык: Английский

Процитировано

37
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

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(7)

Опубликована: Фев. 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.

Язык: Английский

Процитировано

32
Conservation management strategy impacts inbreeding and mutation load in scimitar-horned oryx DOI Creative Commons
Emily Humble, Martin A. Stoffel, Kara Dicks

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(18)

Опубликована: Апрель 25, 2023

In an age of habitat loss and overexploitation, small populations, both captive wild, are increasingly facing the effects isolation inbreeding. Genetic management has therefore become a vital tool for ensuring population viability. However, little is known about how type intensity intervention shape genomic landscape inbreeding mutation load. We address this using whole-genome sequence data scimitar-horned oryx (Oryx dammah), iconic antelope that been subject to contrasting strategies since it was declared extinct in wild. show unmanaged populations enriched long runs homozygosity (ROH) have significantly higher coefficients than managed populations. Additionally, despite total number deleterious alleles being similar across strategies, burden homozygous genotypes consistently groups. These findings emphasize risks associated with mutations through multiple generations As wildlife continue diversify, our study reinforces importance maintaining genome-wide variation vulnerable direct implications one largest reintroduction attempts world.

Язык: Английский

Процитировано

27
From high masked to high realized genetic load in inbred Scandinavian wolves DOI Creative Commons
Linnéa Smeds, Hans Ellegren

Molecular Ecology, Год журнала: 2022, Номер 32(7), С. 1567 - 1580

Опубликована: Дек. 2, 2022

Abstract When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for highly inbred Scandinavian wolf ( Canis lupus ) population, founded only three wolves 1980s suffering from inbreeding depression. We used annotation evolutionary conservation scores study variation total 209 genomes both neighbouring northern Europe. The masked (deleterious heterozygote state) was highest Russia Finland with alleles segregating lower frequency neutral variation. Genetic drift population led loss ancestral alleles, fixation variants significant per‐individual realized homozygote state; an 45% protein‐coding genes) over five generations inbreeding. Arrival immigrants gave temporary rescue effect re‐entering thereby shifting homozygous into genotypes. However, absence permanent connectivity Finnish Russian populations, has then again exposure mutations. These observations provide genome‐wide insight magnitude molecular level, relation history. They emphasize importance securing gene flow management endangered populations.

Язык: Английский

Процитировано

31