The inflated significance of neutral genetic diversity in conservation genetics

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(10)

Published: Feb. 19, 2021

The current rate of species extinction is rapidly approaching unprecedented highs and life on Earth presently faces a sixth mass event driven by anthropogenic activity, climate change ecological collapse. field conservation genetics aims at preserving using their levels genetic diversity, usually measured as neutral genome-wide barometer for evaluating population health risk. A fundamental assumption that higher diversity lead to an increase in fitness long-term survival species. Here, we argue against the perceived importance wild populations We demonstrate no simple general relationship exists between risk extinction. Instead, better understanding properties functional demographic history, relationships, necessary developing implementing effective strategies.

Language: Английский

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The crucial role of genome-wide genetic variation in conservation

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(48)

Published: Nov. 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.

Language: Английский

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The critically endangered vaquita is not doomed to extinction by inbreeding depression

Science, Journal Year: 2022, Volume and Issue: 376(6593), P. 635 - 639

Published: May 5, 2022

In cases of severe wildlife population decline, a key question is whether recovery efforts will be impeded by genetic factors, such as inbreeding depression. Decades excess mortality from gillnet fishing have driven Mexico's vaquita porpoise (

Language: Английский

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Integrating gene annotation with orthology inference at scale

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

Published: April 27, 2023

Annotating coding genes and inferring orthologs are two classical challenges in genomics evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method integrates structural gene annotation orthology inference. implements different paradigm orthologous loci, improves ortholog detection of conserved compared with state-of-the-art methods, handles even highly fragmented assemblies. scales hundreds genomes, which we demonstrate by applying it 488 placental mammal 501 bird assemblies, creating the largest comparative resources so far. Additionally, detects losses, enables selection screens, automatically provides superior measure mammalian genome quality. is powerful scalable annotate compare genomic era.

Language: Английский

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Neutral genetic diversity as a useful tool for conservation biology

Conservation Genetics, Journal Year: 2021, Volume and Issue: 22(4), P. 541 - 545

Published: June 28, 2021

Language: Английский

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The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(3), P. 641 - 652

Published: Dec. 17, 2020

Abstract The quality of genome assemblies has improved rapidly in recent years due to continual advances sequencing technology, assembly approaches, and control. In the field molecular ecology, this led development exceptional that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, population genomics naturally occurring species. Moreover, extent which a single reference represents diversity within species varies: pan‐genomes become increasingly ecological resources, particularly systems found have considerable presence‐absence variation their functional content. Here, we highlight technology raised bar provide guidance on standards achieve genomes. Key recommendations include following: (a) Genome should long‐read except rare cases where it is effectively impossible acquire adequately preserved samples needed high weight DNA standards. (b) At least one scaffolding approach included with such as Hi‐C or optical mapping. (c) carefully evaluated, may involve utilising short read data polishing, error correction, k‐mer analyses, estimating percent reads map back an assembly. Finally, most valuable if all methods are made publicly available utility further verified through examples. While these based current anticipate future push ecology community continue adopt new approaches attain highest assemblies.

Language: Английский

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Reference genomes for conservation

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

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Ancient and historical DNA in conservation policy

Trends in Ecology & Evolution, Journal Year: 2022, Volume and Issue: 37(5), P. 420 - 429

Published: Jan. 24, 2022

Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it rarely included conservation policies and regulations. Even less appreciated is role that ancient historical DNA (aDNA hDNA, respectively) could play unlocking temporal dimension diversity, allowing issues to be resolved, including setting baselines for intraspecies estimating changes effective population size (Ne), identifying genealogical continuity populations. Here, we discuss how information from specimens can central preserving highlight specific incorporate such data help countries meet their CBD obligations.

Language: Английский

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Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

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

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State of knowledge of the population of the vaquita (Phocoena sinus) from the Upper Gulf of California: a bibliometric analysis

Frontiers in Conservation Science, Journal Year: 2025, Volume and Issue: 5

Published: Jan. 7, 2025

The state of scientific knowledge about the vaquita, Phocoena sinus , is presented, a critically endangered endemic species Upper Gulf California, Mexico. Several bibliographic repositories were explored, selecting Web Science because it considers Citation Index as selection criterion. A bibliometric and analysis literature was carried out. network associations built based on co-occurrence sets keywords, which reflect relevance research topics discussed. Two stand out: population conservation. Unaddressed are also identified, such trophic interdependencies, ecosystem, effects environment climate patterns. Regarding population, changes in abundance, vulnerability, distribution current habitat have been addressed. In terms conservation, monotonic decrease size stands out, management aimed at stopping this interaction with commercial illegal fishing. conclusion, measures adopted not effective, given that vaquita continues to decline. There failures application regulations, insufficient monitoring surveillance, unregistered captures, fishing limited participation human communities design implementation perceiving damages lack interest compliance regulations proposed measures. Beyond gained, needed answer key question: ecosystem conditions suitable for recover? question requires different even currently non-existent knowledge.

Language: Английский

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