High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

Pečnerová, Patrícia; Garcia‐Erill, Genís; Liu, Xiaodong; Nursyifa, Casia; Waples, Ryan K.; Santander, Cindy G.; Quinn, Liam; Frandsen, Peter; Meisner, Jonas; Stæger, Frederik Filip; Rasmussen, Malthe Sebro; Brüniche‐Olsen, Anna; Jørgensen, Christian H F; Fonseca, Rute R. da; Siegismund, Hans R.; Albrechtsen, Anders; Heller, Rasmus; Moltke, Ida; Hanghøj, Kristian

doi:10.1016/j.cub.2021.01.064

Cited by 59 publications

(90 citation statements)

References 72 publications

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“…Alternatively, it could suggest relatively small species Ne over a long timescale. Similar declines of Ne estimates right after a lineage split were for instance found in Northern lions (de Manuel et al 2020) and Amur leopards (Pečnerová et al 2021) and were suggested to be the result of founding bottlenecks. The Late Pleistocene was determined by large ice shields covering large parts of Northern Europe and also the Alps (Seguinot et al 2018).…”

Section: Alpine Ibex Show Unique Signals Of Demographic History Compared To Related Speciessupporting

confidence: 67%

“…However, past bottlenecks (times of small population size) are not trivial to estimate. Recent methods based on coalescence theory such as PSMC (Pairwise Sequentially Markovian Coalescent, Li and Durbin 2011) and more recently MSMC (Multiple Sequentially Markovian Coalescent, Schiffels and Wang 2020) have been widely used to estimate the demographic history of species using contemporary DNA and investigate the impact of environmental changes on trajectories of past population size (Palkopoulou et al 2015;Kozma et al 2016;Kozma et al 2018;Pečnerová et al 2021). However, the study of recent DNA is expected to be limited in power due to uncertainty of past diversity, most of all after strong bottlenecks leading to significant loss of signal.…”

Section: Introductionmentioning

confidence: 99%

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Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Robin

Ferrari

Akguel

et al. 2021

Preprint

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Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. A recent bottleneck event can also largely obscure our understanding of standing variation prior to the contraction. Historic population sizes can be modeled based on extant genomics, however uncertainty increases with the severity of the bottleneck. Integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 ± 33 BP to 1919 CE and combine these with 60 published modern genomes. Coalescent demography simulations based on modern genomes indicate population fluctuations matching major climatic change over the past millennia. Using ancient genomes, we show that mitochondrial haplotype diversity has been reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincided with human settlement expansions in the Middle Ages. The near extinction severely reduced the mitochondrial diversity. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Contrary to expectations, we show that a second ancestral mitochondrial lineage has survived in an isolated population further south. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations.

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Section: Alpine Ibex Show Unique Signals Of Demographic History Compared To Related Speciessupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Robin

Ferrari

Akguel

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Alternatively, many researchers are now embracing a hybrid approach, where they sequence a few samples at higher coverage in order to conduct some analyses that require confident genotype calls, and perform the rest of their analyses using lcWGS data from more samples (e.g. Foote et al, 2016; Liu et al, 2014; Pečnerová et al, 2021; Westbury et al, 2018). Furthermore, another promising strategy with a hybrid data set is to form a reference panel using a subset of high‐coverage samples, and impute the genotypes of low‐coverage samples (e.g., Fuller et al, 2020).…”

Section: Current Limitations and Future Developmentsmentioning

confidence: 99%

A beginner's guide to low‐coverage whole genome sequencing for population genomics

et al. 2021

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Despite massive reductions in the cost of DNA sequencing over the past decades, researchers remain faced with decisions about how to distribute sequencing effort along three dimensions: (a) how much of the genome to sequence (breadth of coverage), (b) how deeply to sequence each sample (depth of coverage), and (c) how many samples to sequence. Until recently, reduced-representation sequencing (e.g., RAD-seq [restriction site-associated DNA sequencing]), through which a small random portion of the genome can be sequenced deeply in many individuals to allow for simultaneous variant discovery and high-confidence genotyping, has been the most popular approach for population genomics of nonmodel organisms

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“…Using single genomes to estimate species-wide genetic diversity is problematic because the individuals chosen may not be representative of the species as a whole (e.g., captive individuals (89)). Rather, multiple individuals and populations are necessary to accurately reflect a species' distribution of genetic variation (91,92). Additionally, estimates of genetic diversity are affected by reference genome quality (93), mapping bias (94,95), the methods used to measure genetic variation (e.g., whole genome sequencing, RNAseq, RADseq, SNP array, microsatellites), and bioinformatics approaches (92,93).…”

Section: Is the Relationship Between Genetic Variation And Conservation Status Informative Of The Importance Of Genetic Variation To Popumentioning

confidence: 99%

The crucial role of genome-wide genetic variation in conservation

Kardos

Armstrong

Fitzpatrick

et al. 2021

Preprint

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

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High genetic diversity and low differentiation reflect the ecological versatility of the African leopard

Cited by 59 publications

References 72 publications

Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex

A beginner's guide to low‐coverage whole genome sequencing for population genomics

The crucial role of genome-wide genetic variation in conservation

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