Population Genomics of <i>Daphnia pulex</i>

Lynch, Michael; Gutenkunst, Ryan N.; Ackerman, Matthew S.; Spitze, Ken; Ye, Zhiqiang; Maruki, Takahiro; Jia, Zhiyuan

doi:10.1534/genetics.116.190611

Cited by 61 publications

(99 citation statements)

References 90 publications

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“…To put this in perspective, analysis of a population near the PA locality yields an estimate of π s = 0.0183 for the average within-population silent-site divergence between random alleles (Lynch et al 2016). Because the population from which TCO was obtained is nearly completely inbred (with π s ≈ 0.001; Colbourne et al 2011), a corrected measure of silent-site divergence between the OR and IN D. pulex is 0.0512 − (0.0183/2) = 0.0421 (Nei and Li 1979), reducing the previous time estimates by 18%.…”

Section: Resultsmentioning

confidence: 99%

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

Spitze

et al. 2017

G3 Genes|Genomes|Genetics

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Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with .90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and .60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with 7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome. KEYWORDSgenome annotation effective population size gene number intron mobile elementsThe ultimate goal of comparative genomics is to form a synthesis integrating the fundamental evolutionary forces explaining the variation of genomic architecture across a wide range of phylogenetic lineages. The reduced effective population size (N e ) of eukaryotic species relative to prokaryotic species is hypothesized to be centrally involved in the emergence and distribution of numerous genomic features unique to eukaryotes, and the associated principles should naturally extend to variation among lineages of closely related species (Lynch 2007). However, until recently, it has been difficult to study the impact of reduced N e on the evolution of genomic architecture because of the lack of genomic data from closely related species or populations with disparate population sizes. Moreover, a lack of parallel understanding of other fundamental microevolutionary parameters such as mutation and recombination rates complicates efforts to single out the role of N e (and the associated power of random genetic drift) on genome evolution.Here, we focus on the comparative genomics of two cyclically parthenogenetic Daphnia pulex clones (PA42 and TCO), which come from populations differing substantially in historical N e . The D. pulex species complex consists of a vast array of populations inhabiting hundreds of thousands of ponds and lakes, throughout the northern temperate zone, most of which (including PA42 and TCO) reproduce by repeated generations of clonal reproduction via unfertilized eggs, punctuated by a phase of sexual reproduction. PA42 was sampled from a woodland vernal pond within Portland Arch Nature Preserve, IN, whereas TCO was derived from a permanent pond in the Siuslaw National Forest, near the Pacific coast in OR. A complex geological history in western OR contributes to the presence of divergent lineages of multiple zooplan...

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Section: Resultsmentioning

confidence: 99%

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

Spitze

et al. 2017

G3 Genes|Genomes|Genetics

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104

141

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“…; Lynch et al. ). While selective sweeps may contribute to this pattern, and are indeed required to explain other observations (Campos et al.…”

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“…Importantly, observations from eukaryotic genomes, including humans and mice, show that levels of polymorphism are low in the neighborhood of coding or conserved noncoding sequences and increase approximately monotonically away from them (Cutter and Payseur 2013;Johri et al 2017;Lynch et al 2017). While selective sweeps may contribute to this pattern, and are indeed required to explain other observations (Campos et al 2017), these findings imply that any selective sweeps involved must have rather local effects.…”

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The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018

et al. 2018

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A recent article reassessing the Neutral Theory of Molecular Evolution claims that it is no longer as important as is widely believed. The authors argue that “the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality.” Claiming that “the neutral theory has been overwhelmingly rejected,” they propose instead that natural selection is the major force shaping both between-species divergence and within-species variation. Although this is probably a minority view, it is important to evaluate such claims carefully in the context of current knowledge, as inaccuracies can sometimes morph into an accepted narrative for those not familiar with the underlying science. We here critically examine and ultimately reject Kern and Hahn’s arguments and assessment, and instead propose that it is now abundantly clear that the foundational ideas presented five decades ago by Kimura and Ohta are indeed correct.

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“…All sequence reads were mapped to the reference genome (PA42; Ye et al 2017), derived from a midwest US clone of D. pulex, again as outlined in Lynch et al (2017). As more fully detailed in Maruki et al (in prep.…”

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confidence: 99%

The Recombinational Landscape inDaphnia pulex

Lynch

Maruki

2020

Preprint

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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.

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Population Genomics of Daphnia pulex

Cited by 61 publications

References 90 publications

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018

The Recombinational Landscape inDaphnia pulex

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