The life history fitness of F1 hybrids of the microcrustaceans Daphnia pulex and Daphnia pulicaria (Crustacea, Anomopoda)

Moy, Irene; Green, Makayla; Pham, Thinh Phu; Luu, Dustin Huy-Khang; Xu, Sen

doi:10.1111/ivb.12333

Cited by 3 publications

(1 citation statement)

References 44 publications

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“…To evaluate whether the D. pulicaria private SNPs might result from introgression, we determined the fraction of such SNPs that match known nucleotide variants in the most closely related species, D. pulex, as the two are known to hybridize in the field and in the laboratory (Heier and Dudycha 2009;Vergilino et al 2011;Xu et al 2015;Moy et al 2021). Notably, although 8.6% of D. pulicaria private SNPs are also found in D. pulex, this incidence is twice as enriched (17.3%) in coding regions.…”

Section: Divergence Among Subpopulationsmentioning

confidence: 99%

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Pfrender

Lynch

2023

Preprint

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Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. Here, we compared population-genomics data between D. pulex and D. pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. D. pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, higher incidence of private alleles, and substantially more linkage-disequilibrium than D. pulex. Functional enrichment analysis revealed that positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended lifespan in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Additionally, genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.

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Section: Divergence Among Subpopulationsmentioning

confidence: 99%

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Pfrender

Lynch

2023

Preprint

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Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Ye,

Pfrender,

Lynch

2023

Genome Biology and Evolution

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Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. Here, we compared population-genomic data between D. pulex and D. pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. D. pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, higher incidence of private alleles, and substantially more linkage-disequilibrium than D. pulex. Positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended lifespan in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Additionally, we found that the two species have similar average evolutionary rates at the DNA-sequence level, although ∼160 genes have significantly different rates in the two lineages. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.

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Evolutionary Genomics of a Subdivided Species

Maruki

Lynch

2022

Molecular Biology and Evolution

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The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of ten populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation by distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼ 650, 000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.

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The life history fitness of F₁ hybrids of the microcrustaceans Daphnia pulex and Daphnia pulicaria (Crustacea, Anomopoda)

Cited by 3 publications

References 44 publications

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Evolutionary Genomics of a Subdivided Species

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