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+[[!meta title="The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability"]]
+[[!tag mutation]]
+
+The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability
+
+Ruyun Deng, Feng Guo, Wen Wei, Michael E. Pfrender, Jeff L. Dudycha, Michael Lynch, Zhiqiang Ye
+
+bioRxiv 2025.09.17.676786; doi:10.1101/2025.09.17.676786
+
+[[!doi 10.1101/2025.09.17.676786v1 desc="“For D. pulex, the estimated mutation rates range from 2.3 × 10⁻⁹ to 4.53 × 10⁻⁹ substitutions per site per generation […] the estimate for D. magna is somewhat higher, ~8.9 × 10⁻⁹ per site per generation.” “Genetically, D. obtusa is moderately divergent from the D. pulex–D. pulicaria species complex, with a silent-sit divergence of ~0.12” “The primary draft genome assembly presented here, FS6_V2, consists of 129.4 Mb of DNA sequences located on 12 chromosomes” “over 20 years […], 142 eight lines survived for deep whole-genome sequencing, having been propagated asexually for an average of 482 generations” “we restricted our analysis to genomic sites with read depths between 20 and 300, resulting in an average of 87 million callable sites per sample” “Across the D. obtusa genome, 99.43% of sites were homozygous, with only 0.57% being heterozygous” “we defined a de novo mutation as a site that was unique to a single MA line and represented a change from the ancestral homozygous state to a heterozygous state” “The overall SNM rate is estimated to be 2.23 × 10−9 mutations per base per generation […] while the indel rate is 2.75 × 10−10” “Among the base substitutions, the most frequent type is C:G > T:A, occurring at a frequency 5.6 × higher than the least common type, C:G > G:C. The transition-to-transversion (Ts/Tv) ratio is 1.31” “To estimate the expected GC-content of the genome at mutation–equilibrium, we used the rate of G/C → A/T substitutions (v) and the rate of A/T → G/C substitutions (u). The equilibrium GC-content […] is calculated as u / (u + v) [and was] estimated to be 0.320, which is much lower than the observed GC content of 0.409.” “ we observed a significant deficit of mutations at nonsynonymous sites”. “While chromosomes 11 and 12 showed slightly elevated mutation rates, a Chi-square test indicated no significant deviation from a uniform distribution”. “Using a minor allele frequency (MAF) threshold of >0.02 to define the presence of alternative alleles, we found that 210 (29%) and 248 (34%) of the SNMs from the MA lines were also present in the EBG and RAP populations” “we identified a total of 48 LOH events, with the number of events per MA line ranging from 0 to 22” “We estimated a genome-wide LOH rate of 2.93 × 10−5 per heterozygous site per generation.” “Among the 48 identified LOH events, 8 were attributed to heterozygous deletions, while 40 were attributed to gene conversion. The average length of conversion tracts was 320 kb. The estimated genome-wide rate of conversion-induced LOH was 2.62 × 10−5 per heterozygous site per generation.”"]]
[[!meta title="pages tagged mutation"]]
-De novo mutation rate in _Branchiostoma floridae_ was estimated to 5.10 × 10-9 per base per generation by [[Xue and coll. (2025)|biblio/10.1101_2025.07.14.664012]]
+### De novo mutation rates
+
+_Branchiostoma floridae_ was estimated to 5.10 × 10-9 per base per generation by [[Xue and coll. (2025)|biblio/10.1101_2025.07.14.664012]]
+
+_Daphnia obtusa_: [[Deng and coll. (2025)|biblio/10.1101_2025.09.17.676786v1]] estimated a spontaneous single nucleotide mutation (SNM) rate of 2.23 × 10-9 and an indel mutation rate of 2.75 × 10-10 per site per generation“ using mutation accumulation lines.
[[!inline pages="tagged(mutation)" actions="no" limit=0]]
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