GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Kutschera, Verena E.; Kierczak, Marcin; Valk, Tom van der; Seth, Johanna von; Dussex, Nicolás; Lord, Edana; Dehasque, Marianne; Stanton, David W. G.; Khoonsari, Payam Emami; Nystedt, Björn; Dalén, Love; Díez-del-Molino, David

doi:10.1101/2022.03.04.482637

Cited by 7 publications

(12 citation statements)

References 49 publications

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“…The assessment of extinction rate should be based on the best-available data and methods to evaluate all aspects of genomic erosion, and not just genetic diversity. Given their high technical complexity, we believe these analyses should be done in a standardised way 112,114 and with a common set of metrics 115 to help translate this knowledge into conservation management action 116,117,118 . A database that quantifies genomic erosion is likely to become instrumental in underpinning future conservation efforts to help stem the biodiversity crisis in the UN’s Decade on Ecosystem Restoration and beyond.…”

Section: Discussionmentioning

confidence: 99%

Genomic erosion in the assessment of species extinction risk and recovery potential

Oosterhout

Speak

Birley

et al. 2022

Preprint

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Many species are facing unprecedented population size declines and deterioration of their environment. This exposes species to genomic erosion, which we define here as the damage inflicted to a species' genome or gene pool due to a loss of genetic diversity, an increase in expressed genetic load, maladaptation, and/or genetic introgression. The International Union for Conservation of Nature (IUCN) bases its extinction risk assessments on direct threats to population size and habitat. However, it does not assess the long-term impacts of genomic erosion, and hence, it is likely to underestimate the extinction risk of many species. High-quality whole genome sequence data that is currently being generated could help improve extinction risk assessments. Genomic data contains information about a species' past demography, its genome-wide genetic diversity, the incidence of genetic introgression, as well as the genetic load of deleterious mutations. Computer modelling of these data enables forecasting of population trajectories under different management scenarios. In this Perspective, we discuss the threats posed by genomic erosion. Using evolutionary genomic simulations, we argue that whole-genome sequence data provides critical information for assessing species extinction risk and recovery potential. Genomics-informed assessments of the extinction risk complement the IUCN Red List, and such genomics-informed conservation is invaluable in guiding species recovery programs in the UN's Decade on Ecosystem Restoration and beyond.

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Section: Discussionmentioning

confidence: 99%

Genomic erosion in the assessment of species extinction risk and recovery potential

Oosterhout

Speak

Birley

et al. 2022

Preprint

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“…Raw resequencing data was demultiplexed using bcl2Fastq v2.17.1 (Illumina Inc.), and then trimmed and mapped to the reference de novo genome using a development version of GenErode ( https://github.com/NBISweden/GenErode , [ 54 ]), where adapters were removed using a modified version of SeqPrep v1.1 ( https://github.com/jstjohn/SeqPrep ) as per [ 34 ]. Endogenous DNA content for all 59 samples was estimated from the BAM files prior to duplicate removal.…”

Section: Methodsmentioning

confidence: 99%

Population dynamics and demographic history of Eurasian collared lemmings

Lord

Marangoni²,

Baca³

et al. 2022

BMC Ecol Evo

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Background Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. Results Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. Conclusions This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.

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“…Finally, we identified repeats using repeatmodeler v1.0.11 and repeatmasker v4.0.7 [Smit, A.F.A. and Hubley, R. (2008–2015) RepeatModeler Open-1.0, http://www.repeatmasker.org/ ] and CpG sites using the GenErode bioinformatics pipeline [ 82 ].…”

Section: Methodsmentioning

confidence: 99%

“…Mapping and variant calling for historical and modern data was done using a beta version of the GenErode bioinformatics pipeline [ 82 ]. Briefly, adapter trimming was done with trimmomatic v0.32 [ 83 ] for modern samples while we used Seqprep v1.1 ( https://github.com/jstjohn/SeqPrep ) to trim and merge forward and reverse reads for historical samples.…”

Section: Methodsmentioning

confidence: 99%

Genomic trajectories of a near-extinction event in the Chatham Island black robin

et al. 2022

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Background Understanding the micro-evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation. Results We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations. Conclusion Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.

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GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Cited by 7 publications

References 49 publications

Genomic erosion in the assessment of species extinction risk and recovery potential

Genomic erosion in the assessment of species extinction risk and recovery potential

Population dynamics and demographic history of Eurasian collared lemmings

Genomic trajectories of a near-extinction event in the Chatham Island black robin

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