Self-fertilization sweeps up variation in the worm genome

Phillips, Patrick C.

doi:10.1038/ng.2201

Cited by 6 publications

(6 citation statements)

References 9 publications

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“…Self-reproduction leads to increased homozygosity and linkage disequilibrium, which is known from theory [ 25 – 27 , 29 , 122 , 133 – 135 ] and which has been frequently shown empirically (reviewed in [ 136 ]). For Caenorhabditis nematodes, genomic landscapes of diversity have already been derived for three selfing species [ 50 , 71 , 72 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

et al. 2023

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Caenorhabditis nematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducing Caenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematode C. remanei. We demonstrate that the genomic distribution of recombination in C. remanei, like the model nematode C. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being tenfold greater for C. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. The results illustrate how genome organization and selection play a crucial role in shaping the genomic pattern of diversity whereas demographic processes scale the level of diversity across the genome as a whole.

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Section: Discussionmentioning

confidence: 99%

Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

et al. 2023

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“…Those rotting fruits were collected primarily in human-built orchards; although rotting stems are found in natural preserves, primary forests no longer exist in Europe [13]. Like many other model organisms ( Drosophila melanogaster , Saccharomyces cerevisiae , Mus musculus ), C. elegans is thus at least partly human-associated, which likely exerts a strong influence on its range, migration patterns, and population structure [5,14,15]. However, we still have very limited information on the distribution of C. elegans and other Caenorhabditis species relating to habitat type and geographic location.…”

Section: Introductionmentioning

confidence: 99%

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

et al. 2013

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BackgroundIn stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence.MethodsHere we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana.ResultsSampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales.ConclusionsThe abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted groups. Local samples for the cosmopolitan C. briggsae mirror its pan-tropical patterns of intraspecific polymorphism. It remains an important challenge to decipher what drives Caenorhabditis distributions and diversity within and between species.

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“…Self-reproduction leads to increased homozygosity and linkage disequilibrium, which is known from theory ([31], [32], [33], [35], [134], [135], [136], [122]) and which has been frequently shown empirically (reviewed in [137]). For Caenorhabditis nematodes, genomic landscapes of diversity have already been derived for three selfing species ([66], [73], [74]).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity landscapes in outcrossing and selfingCaenorhabditisnematodes

Teterina

Willis

Lukac

et al. 2022

Preprint

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Caenorhabditisnematodes form an excellent model for studying how the mode of reproduction affects genetic diversity, as some species reproduce via outcrossing whereas others can self-fertilize. Currently, chromosome-level patterns of diversity and recombination are only available for self-reproducingCaenorhabditis, making the generality of genomic patterns across the genus unclear given the profound potential influence of reproductive mode. Here we present a whole-genome diversity landscape, coupled with a new genetic map, for the outcrossing nematodeC. remanei. We demonstrate that the genomic distribution of recombination inC. remanei, like the model nematodeC. elegans, shows high recombination rates on chromosome arms and low rates toward the central regions. Patterns of genetic variation across the genome are also similar between these species, but differ dramatically in scale, being 10-fold greater forC. remanei. Historical reconstructions of variation in effective population size over the past million generations echo this difference in polymorphism. Evolutionary simulations demonstrate how selection, recombination, mutation, and selfing shape variation along the genome, and that multiple drivers can produce patterns similar to those observed in natural populations. Convolutional neural networks demonstrate the potential for classifying distinct evolutionary scenarios in simulated populations. Distinguishing these forces confidently with the empirical data, however, will benefit from larger population genomic samples from multiple populations and consideration of an even more extensive training set of simulations.

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Self-fertilization sweeps up variation in the worm genome

Abstract: A new study reports a comprehensive survey of genetic diversity in natural populations of the nematode C. elegans. They suggest that recent chromosome-scale selective sweeps have reduced C. elegans genetic diversity worldwide and strongly structured genetic variation across its genome.

Cited by 6 publications

References 9 publications

Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes

Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

Genetic diversity landscapes in outcrossing and selfingCaenorhabditisnematodes

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