Challenges in quantifying genome erosion for conservation

Bosse, Mirte; Loon, Sam van

doi:10.3389/fgene.2022.960958

Cited by 17 publications

(12 citation statements)

References 186 publications

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“…Genetic diversity is one component of genomic erosion and important for species persistence and adaptation and is currently recognized as one of the three relevant levels of biological diversity by the Convention on Biological Diversity (CBD, O'Brien et al, 2022). Genetic diversity is relatively simple to determine from a small number of samples with a handful of genetic markers (Bosse and Loon, 2022). However, genomic heterogeneity in genetic diversity (Robinson et al, 2019) and its functional relevance to species persistence and adaptation (Teixeira and Huber, 2021) are from clear.…”

Section: Discussionmentioning

confidence: 99%

The last days ofAporia crataegi(L.) in Britain: evaluating genomic erosion in an extirpated butterfly

Whitla,

Hens,

Hogan

et al. 2023

Preprint

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Current rates of climate change and habitat degradation are causing biodiversity declines globally, with global extinction rates far beyond estimated background extinction rates. Studies on vertebrates highlight how conservation genomics can be an effective tool to identify and manage threatened populations. However, it is unclear how metrics of genomic erosion, commonly applied in conservation genomics, translate to invertebrate species which can have markedly different population sizes and life history strategies. The Black-veined White butterfly (Aporia crataegi)was extirpated from Britain in the 1920s. Here, we sequenced historical DNA from 17 museum specimens collected between 1854 and 1924 to determine levels of genomic erosion in the species as it approached extirpation. We compare these results to those from the Common Blue butterfly (Polyommatus icarus) - a species with stable demographic trends in Great Britain. We provide evidence for a bottleneck of British butterflies around the period of post-glacial colonisation of the British Isles. Despite a 4X difference in effective population sizes around the time of post-glacial colonisation, reduction in genome-wide heterozygosity (our metric for genetic diversity) inA. crataegi(17.9%) was comparable to that inP. icarus(14.5%). More symptomatic ofA. crataegi’s disappearance were marked increases in size and proportion of runs-of-homozygosity (RoH) and accumulation of putatively mildly and weakly deleterious variants. Our results support the notion that metrics with more direct links to host fitness and function, such as inbreeding and genetic load, may be more informative of population decline and thus more valuable in identifying vulnerable insect populations.

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Section: Discussionmentioning

confidence: 99%

The last days ofAporia crataegi(L.) in Britain: evaluating genomic erosion in an extirpated butterfly

Whitla,

Hens,

Hogan

et al. 2023

Preprint

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“…Besides the reduced adaptivity, the highly enhanced inbreeding rate will lead to the accumulation of “negative” mutations that reduce the fitness of the few surviving individuals. The degeneration of the genomes of threatened species has been summarized under the term “genome erosion”, integrating overall homozygosity, genetic load, and runs of homozygosity (Bosse & van Loon, 2022). However, quantification of genome erosion has been recognized to be challenging, although it is crucial to understand the detection of genomic health in species experiencing rapid habitat loss and fragmentation.…”

Section: The Genetics Of Extinction—a Poorly Understood Processmentioning

confidence: 99%

“…Action plans aiming to protect highly threatened species benefit substantially by integrating reference genomes of these species (Brandies et al, 2019; Hogg et al, 2022; Paez et al, 2022; Wang et al, 2022). Species experiencing rapid decline in number of individuals are prone to highly enhanced extinction threats as the consequence of genome erosion (Hogenloge et al, 2020; Bosse & van Loon, 2022; Tian & Ma, 2021). Furthermore, the increased frequency of negative mutations undermines the success of breeding programs aiming to expand the number of individuals, in particular by the enhanced rate of inbreeding.…”

Section: Rationale Of Initiative 1—generating Reference Genomes Of Hi...mentioning

confidence: 99%

Integrating genomics and conservation to safeguard plant diversity

Schneider

2023

Integrative Conservation

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Conserving genetic diversity has been increasingly recognized as a keystone towards the protection of biodiversity and natural resources for future generations of humankind. In turn, the ongoing genomic revolution provides us with the technical innovations and expanded knowledge required to establish programs to integrate genomic approaches into programs to protect plant diversity and its genetic diversity. Although obtaining whole genomes of all organisms is still a far‐fetched dream, rapid progress in assembling whole genomes across the plant tree‐of‐life has provided access to reference genomes for many plants but, unfortunately, not all lineages of the plant tree‐of‐life. Addressing the existing taxon gaps is arguably best achieved by focusing on the genomes of plant species that experience high extinction threats or play a crucial role in ecosystem restoration. This review summarizes not only the recent progress in plant genomics with an emphasis on their importance to the conservation of plant diversity but also outlines steps to integrate genomics into plant conservation. Given the complexity of threats driving plant extinction, such as reduced genetic diversity, enhanced genome erosion, and loss of species integrity by hybridization, the integration of genomic research into our conservation efforts is crucial to understand extinction processes and, most importantly, to support the targets set to achieve “Harmony with Nature.”

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“…These extinction-related dynamics can be detected as reduction in heterozygosity, elevated ratios of P n / P s (number of nonsynonymous polymorphisms/number of synonymous polymorphisms), and long runs of homozygosity (ROH). However, factors such as different demographic histories or generation intervals can lead to differing levels and patterns of genome erosion signals among declining taxa ( Bosse and van Loon 2022 ). For instance, depending on the nature of population decline, such as sudden bottlenecks, repeated founder effects, or long-term small effective population size ( N e ), one may or may not observe a deflated P n / P s ratio; this is because the decline in the force of purifying selection caused by bottlenecks and the purging of recessive deleterious genetic load under sustained small N e can have opposing effects ( Bertorelle et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages

Atağ,

Kaptan,

Yüncü

et al. 2024

Genome Biology and Evolution

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Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the IUCN. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them to eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (Ovis gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity (ROH) blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne as well as mutation load estimates are lower in Cyprian compared to Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages, and a limited consistency between viability metrics and IUCN conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.

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Challenges in quantifying genome erosion for conservation

Cited by 17 publications

References 186 publications

The last days ofAporia crataegi(L.) in Britain: evaluating genomic erosion in an extirpated butterfly

The last days ofAporia crataegi(L.) in Britain: evaluating genomic erosion in an extirpated butterfly

Integrating genomics and conservation to safeguard plant diversity

Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages

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