Direct estimate of the spontaneous germ line mutation rate in African green monkeys

Pfeifer, Susanne

doi:10.1111/evo.13383

Cited by 46 publications

(75 citation statements)

References 105 publications

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“…Some studies use the deviation from 50 % of the de novo mutation pass to the next generation to infer the false-positive rate (Jónsson et al 2017;Thomas et al 2018). Others use probabilistic methods to access the callability (Besenbacher et al 2019), or simulation of known mutation to control the pipeline quality (Pfeifer 2017). Differences in methods likely impact the calculated rate.…”

Section: Discussionmentioning

confidence: 99%

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

Bergeron

Besenbacher

Bakker

et al. 2020

Preprint

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32Understanding the rate and pattern of germline mutations is of fundamental importance for 33 understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques 34 (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average 35 r a t e of 0.73 × 10 −8 de novo mutations per site per generation (95 % CI: 0.65 × 10 −8 -0.81 × 36 10 −8 ). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is 37 positively correlated with the paternal age. The paternal lineage contributed an average of 80 % of 38 the de novo mutations, with a trend of an increasing male contribution for older fathers. About 1.9 39 % of de novo mutations were shared between siblings, with no parental bias, suggesting that they 40 arose from early development (postzygotic) stages. Finally, the divergence times between closely 41 related primates calculated based on the yearly mutation rate of rhesus macaque generally 42 reconcile with divergence estimated with molecular clock methods, except for the 43 Cercopithecidae/Hominoidea molecular divergence dated at 54 Mya using our new estimate of the 44 yearly mutation rate. 45

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Section: Discussionmentioning

confidence: 99%

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

Bergeron

Besenbacher

Bakker

et al. 2020

Preprint

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“…PCR reactions were run in 25 µl final 106 volume containing 1U GoTaq G2 Green Master Mix, 0.33 µM of each primer (forward and reverse, 107 Table S1), 2 µl of genomic DNA and 6.5 µl ddH20. The cycling conditions followed the procedure 108 recommended by Haus et al 2013 with a few modifications to the annealing temperatures of each 109 (https://github.com/lh3/seqtk.git ) and we then ran hPSMC on artificial hybrids of all pairwise 163 combination between Dryas monkey and the vervets (using four different vervet genomes per species) 164 assuming a generation time of 8.5 years (Warren et al, 2015) and a mutation rate per generation of 165 0.94x10 -8 (Pfeifer, 2017). 166 167 2.5| Mitochondrial phylogeny 168…”

Section: 3| Cytochrome B Sequencing 104mentioning

confidence: 99%

The genome of the endangered Dryas monkey provides new insights into the evolutionary history of the vervets

Valk

Gonda

Hart³

et al. 2019

Preprint

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13Genomic data can be a powerful tool for inferring ecology, behaviour and conservation needs of highly 14 elusive species, particularly when other sources of information are hard to come by. Here we focus on 15 the Dryas monkey (Cercopithecus dryas), an endangered primate endemic to the Congo Basin with 16 cryptic behaviour and possibly less than 250 remaining individuals. Using whole genome sequencing 17 data we show that the Dryas monkey represents a sister lineage to the vervets (Chlorocebus sp.) and 18 has diverged from them around 1.4 million years ago with additional bi-directional gene flow ~750,000 19 -~500,000 years ago that has likely involved the crossing of the Congo River. Together with evidence 20 of gene flow across the Congo River in bonobos and okapis, our results suggest that the fluvial topology 21 of the Congo River might have been more dynamic than previously recognised. Despite the presence 22 of several homozygous loss-of-function mutations in genes associated with sperm mobility and 23 immunity, we find high genetic diversity and low levels of inbreeding and genetic load in the studied 24 Dryas monkey individual. This suggests that the current population carries sufficient genetic variability 25 for long-term survival and might be larger than currently recognised. We thus provide an example of 26 how genomic data can directly improve our understanding of highly elusive species.

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“…However, unrepaired mutations, while rare, do occur and can increase with parental age in both sexes [52,[65][66][67]. Robust estimates of germline mutation rates are still limited, but overall they appear to occur at a higher rate in humans and other primates than in the other vertebrate and invertebrate taxa that have been studied [68][69][70][71]. Most detailed information comes from studies of humans and mice.…”

Section: Causes Of Germline Deteriorationmentioning

confidence: 99%

The deteriorating soma and the indispensable germline: gamete senescence and offspring fitness

2019

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The idea that there is an impenetrable barrier that separates the germline and soma has shaped much thinking in evolutionary biology and in many other disciplines. However, recent research has revealed that the so-called ‘Weismann Barrier’ is leaky, and that information is transferred from soma to germline. Moreover, the germline itself is now known to age, and to be influenced by an age-related deterioration of the soma that houses and protects it. This could reduce the likelihood of successful reproduction by old individuals, but also lead to long-term deleterious consequences for any offspring that they do produce (including a shortened lifespan). Here, we review the evidence from a diverse and multidisciplinary literature for senescence in the germline and its consequences; we also examine the underlying mechanisms responsible, emphasizing changes in mutation rate, telomere loss, and impaired mitochondrial function in gametes. We consider the effect on life-history evolution, particularly reproductive scheduling and mate choice. Throughout, we draw attention to unresolved issues, new questions to consider, and areas where more research is needed. We also highlight the need for a more comparative approach that would reveal the diversity of processes that organisms have evolved to slow or halt age-related germline deterioration.

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Direct estimate of the spontaneous germ line mutation rate in African green monkeys

Cited by 46 publications

References 105 publications

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

The germline mutational process in rhesus macaque and its implications for phylogenetic dating

The genome of the endangered Dryas monkey provides new insights into the evolutionary history of the vervets

The deteriorating soma and the indispensable germline: gamete senescence and offspring fitness

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