Genome-wide diversity loss in reintroduced Eurasian lynx populations urges immediate conservation management

Mueller, Sarah Ashley; Prost, Stefan; Anders, Ole; Breitenmoser‐Würsten, Christine; Kleven, Oddmund; Klinga, Peter; Konec, Marjeta; Kopatz, Alexander; Krojerová-Prokešová, Jarmila; Middelhoff, Tomma Lilli; Obexer-Ruff, Gabriela; Reiners, Tobias Erik; Schmidt, Krzysztof; Sindičić, Magda; Skrbinšek, Tomaž; Tám, Branislav; Saveljev, Alexander P.; Galsandorj, Naranbaatar; Nowak, Carsten

doi:10.1016/j.biocon.2021.109442

Cited by 20 publications

(36 citation statements)

References 64 publications

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“…In addition, we used the softwares recommended default settings for ROHs calling. We note that previous studies (Duntsch et al, 2021;Meyermans et al, 2020;Mueller et al, 2022) showed that changing these settings could lead to different results. For instance, Mueller et al, (2022) showed adapting parameters might allow to get similar results between WGS and reduced genomic representations with smaller fractions of genomes: the authors used PLINK to call ROHs with RAD-sequencing.…”

Section: Limitationsmentioning

confidence: 76%

“…We note that previous studies (Duntsch et al, 2021;Meyermans et al, 2020;Mueller et al, 2022) showed that changing these settings could lead to different results. For instance, Mueller et al, (2022) showed adapting parameters might allow to get similar results between WGS and reduced genomic representations with smaller fractions of genomes: the authors used PLINK to call ROHs with RAD-sequencing. They then tested ROH calling with several different settings for three individuals for which they also had WGS data and extracted the settings which best conserved the rank of inbreeding found with WGS.…”

Section: Limitationsmentioning

confidence: 76%

“…However, many studies performing ROHs analyses with PLINK use reduced genomic representation techniques: ROHs have been very often called with SNP arrays (Bjelland et al, 2013; Bosse et al, 2012; de Jong et al, 2020; Forutan et al, 2018) where specific SNPs, chosen based on their position, effect on phenotype or Minor Allele Frequency (MAF), are targeted and sequenced. ROHs have also been called with Restriction-Site Associated DNA Sequencing (RAD-sequencing) (Grossen et al, 2018; Mueller et al, 2022) data, by cutting the genome near enzymes cutting sites and then selecting and sequencing fragments based on their size. With both SNP arrays and RAD sequencing, only a (small) fraction of the genome is sequenced resulting in a partial representation of the total polymorphism.…”

Section: Introductionmentioning

confidence: 99%

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Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

Lavanchy

Goudet

2022

Preprint

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Runs of homozygosity (ROHs) are proxy for genomic Identical-by-Descent segments and are increasingly used to measure individual inbreeding. ROHs analyses are mostly carried out on SNPs-arrays and whole-genome-sequencing data. Softwares recurrently used for their detection usually assume that genomic positions which have not been genotyped are non-variant. This might be true for whole-genome-sequencing data, but not for reduced genomic representations and can lead to spurious ROHs detection. We simulated the outputs of whole-genome-sequencing, two SNP-arrays and RAD-sequencing for three populations with different sizes. We compare the results of ROHs calling with two softwares: PLINK and RZooRoH. We demonstrate that to obtain meaningful estimates of inbreeding coefficients, RZooRoH requires fraction of genome seven times smaller compared to PLINK. When the SNP density is above 20 SNPs/Mb for PLINK and 3 SNPs/Mb for RZooRoH, ranks of ROHs-based inbreeding coefficients are conserved among individuals. With reduced genomic representations, ROHs distributions are consistently biased towards an underestimation of the total numbers of small and an overestimation of the total numbers of large ROHs, except for RZooRoH and high-density SNPs-arrays. We conclude that both ROHs-based inbreeding coefficients and ROHs distributions exact quantification are highly dependent on the fraction of genome sequenced and should thus be treated with caution. However, relative inbreeding estimates, such as comparison between individuals or populations, are reliable with reduced genomic representations providing that the fraction of genome sequenced is large enough. Consequently, we advise researchers working with reduced genomic data to use SNPs-independent measures or model-based ROHs calling methods for inbreeding estimations.

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Section: Limitationsmentioning

confidence: 76%

Section: Limitationsmentioning

confidence: 76%

Section: Introductionmentioning

confidence: 99%

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Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

Lavanchy

Goudet

2022

Preprint

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“…Most of the lynx populations occurring in the southern region originate from reintroductions (except for the ones in Poland, North Macedonia, and Turkey), an ongoing process starting in the 1970s, but the genetic origin is mostly from the same region, i.e., the Carpathian Mountains. However, lynx in the Harz mountains in Germany descend from zoo stock, which includes Baltic/Scandinavian, Siberian, and Carpathian origin (Linnell et al, 2009 ; Mueller et al, 2022 ). Sample size was relatively even between the regions (>65°N = 101 events, 65–55°N = 109, and <55°N = 103).…”

Section: Methodsmentioning

confidence: 99%

Timing and synchrony of birth in Eurasian lynx across Europe

Mattisson

Linnell

Anders

et al. 2022

Ecology and Evolution

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The ecology and evolution of reproductive timing and synchrony have been a topic of great interest in evolutionary ecology for decades. Originally motivated by questions related to behavioral and reproductive adaptation to environmental conditions, the topic has acquired new relevance in the face of climate change. However, there has been relatively little research on reproductive phenology in mammalian carnivores. The Eurasian lynx ( Lynx lynx ) occurs across the Eurasian continent, covering three of the four main climate regions of the world. Thus, their distribution includes a large variation in climatic conditions, making it an ideal species to explore reproductive phenology. Here, we used data on multiple reproductive events from 169 lynx females across Europe. Mean birth date was May 28 (April 23 to July 1), but was ~10 days later in northern Europe than in central and southern Europe. Birth dates were relatively synchronized across Europe, but more so in the north than in the south. Timing of birth was delayed by colder May temperatures. Severe and cold weather may affect neonatal survival via hypothermia and avoiding inclement weather early in the season may select against early births, especially at northern latitudes. Overall, only about half of the kittens born survived until onset of winter but whether kittens were born relatively late or early did not affect kitten survival. Lynx are strict seasonal breeders but still show a degree of flexibility to adapt the timing of birth to surrounding environmental conditions. We argue that lynx give birth later when exposed to colder spring temperatures and have more synchronized births when the window of favorable conditions for raising kittens is shorter. This suggests that lynx are well adapted to different environmental conditions, from dry and warm climates to alpine, boreal, and arctic climates. This variation in reproductive timing will be favorable in times of climate change, as organisms with high plasticity are more likely to adjust to new environmental conditions.

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“…For example, the settings best suited for inferring ROHs in a small, long-isolated population experiencing high levels of inbreeding would not be suitable for individuals sampled from a large, genetically diverse population because underlying sources of error in these two scenarios are very different (e.g., differences in ROH length distributions, numbers of variable sites, expected minor allele frequencies; Ceballos, Joshi, Clark, Ramsay, & Wilson, 2018). While some studies include comparisons of results from multiple programs or parameter value combinations (e.g., Saremi et al, 2019;Grossen, Guillaume, Keller, & Croll, 2020;von Seth et al, 2021;Mueller et al, 2022), many more studies rely on default settings and do not explore the effects of varying these parameter values on their results. Without extensive knowledge of a population's demographic history (e.g., prevalence and degree of consanguineous mating or immigration), it can be challenging to determine the most appropriate combination of parameter values, and it is always impossible to know how close the resulting estimates approximate reality.…”

Section: Introductionmentioning

confidence: 99%

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history

Harder

Kirksey

Mathur

et al. 2022

Preprint

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Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. However, selecting an appropriate program and parameter values for such analyses is often difficult for species of conservation concern, for which little is often known about population demographic histories or few high-quality genomic resources are available. Herein, we analyze simulated and empirical data sets to demonstrate the downstream effects of program selection on ROH inference. We also apply a sensitivity analysis to evaluate the effects of various parameter values on ROH-calling results and demonstrate its utility for parameter value selection. We show that ROH inferences can be biased when sequencing depth and the distribution of ROH length is not interpreted in light of program-specific tendencies. This is particularly important for the management of endangered species, as some program and parameter combinations consistently underestimate inbreeding signals in the genome, substantially undermining conservation initiatives. Based on our conclusions, we suggest using a combination of ROH detection tools and ROH length-specific inferences to generate robust population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort typical of conservation genomics studies.

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Genome-wide diversity loss in reintroduced Eurasian lynx populations urges immediate conservation management

Cited by 20 publications

References 64 publications

Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization

Timing and synchrony of birth in Eurasian lynx across Europe

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history

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