The Recombinational Landscape inDaphnia pulex

Abstract

Through the analysis of linkage disequilibrium from genome-wide sequencing data for multiple individuals from eight populations, the general features of the recombinational landscape are revealed in the microcrustacean Daphnia pulex. The data suggest an exceptionally uniform pattern of recombination across the genome, while also confirming general patterns that are inconsistent with existing population-genetic models for the relationship between linkage disequilibrium and physical distances between genomic sites. Patterns of linkage disequilibrium are highly consistent among populations, and average rates of recombination are quite similar for all chromosomes. There is no evidence of recombination hotspots, and although there does appear to be suppressed recombination in the vicinity of gene bodies, this effect is quite small.Although this species reproduces asexually in ∼ 80% of generations, the mean per-generation recombination rate per nucleotide site is ∼ 37× the per-nucleotide mutation rate. Contrary to expectations for models in which crossing-over is the primary mechanism of recombination, and consistent with data for other species, the gradient of linkage disequilibrium with increasing physical distance between sites is far too high at short distances and far too low at long distances, suggesting an important role for factors such as the nonindependent appearance of pairs of mutations on haplotypes and long-range gene-conversion-like processes. Combined with other observations on patterns of nucleotide variation, these results provide a strong case for the utility of D. pulex as a model system for the study of mechanisms of evolution in natural populations.

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

“…However, in eukaryotes, reports of mutation rates below 10 −9 are restricted to unicellular species 49 . Second, mitotic recombination and gene conversion can also contribute to LD decay (it is noteworthy that gene conversion was recently proposed to be an important determinant of LD patterns in cyclically parthenogenetic Daphnia pulex 50 ). This could affect our calculations based on the assumption that the only source of LD decay is reciprocal meiotic recombination and consequently bias upwards estimates of the prevalence of meiosis.…”

Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes ofDaphnia pulex,Daphnia pulicaria, andDaphnia obtusa

“…The correlation between genome-wide mitochondrial and nuclear synonymous-site diversities (obtained from Maruki et al 2022 ) among the 10 NA Midwest D. pulex populations is not significant (linear regression: r 2 = 0.014, P = 0.74). Given the typically uniparental nature of mitochondrial inheritance, this is unsurprising, as the organelle genome effectively represents one degree of freedom relative to the large number of effectively freely recombining and segregating sites in the nuclear genome (essentially all pairs of sites >1 Mb apart; Lynch et al 2022 ).…”

The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex

“…These results are mirrored in D . pulex for which both population genomic and sperm‐based estimates have been produced (Lynch et al, 2020; Xu, Ackerman, et al, 2015). Our results are in general agreement with these previous studies; however, we did find several instances where large parts of linkage group arms exhibited suppressed recombination spanning several megabases (e.g., Figure 1).…”

“…For example, genetic maps constructed from an F 2 panel for Daphnia magna showed universally high recombination near the chromosome ends and suppressed recombination in the chromosome centres (Dukić et al, 2016). These results are mirrored in D. pulex for which both population genomic and sperm-based estimates have been produced (Lynch et al, 2020;. Our results are in general agreement with these previous studies; however, we did find several instances where large parts of linkage group arms exhibited suppressed recombination spanning several megabases (e.g., Figure 1).…”