2022
DOI: 10.1093/molbev/msac059
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Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes ofDaphnia pulex,Daphnia pulicaria, andDaphnia obtusa

Abstract: Genetic variants of mitochondrial DNA (mtDNA) at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, D. pulicaria, and D. obtusa. Extensive heteroplasmy is obse… Show more

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Cited by 11 publications
(15 citation statements)
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“…However, North American D. pulex and D. pulicaria are not reciprocally monophyletic (Supplemental Figure 2). The recent split-time between North American D. pulex and D. pulicaria (Ye et al, 2022), their propensity to hybridize (Pantel et al, 2011), and discordant mitochondrial and nuclear phylogenies support the hypothesis that North American taxa are in the process of incipient speciation (Heier & Dudycha, 2009).…”
Section: Resultsmentioning
confidence: 76%
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“…However, North American D. pulex and D. pulicaria are not reciprocally monophyletic (Supplemental Figure 2). The recent split-time between North American D. pulex and D. pulicaria (Ye et al, 2022), their propensity to hybridize (Pantel et al, 2011), and discordant mitochondrial and nuclear phylogenies support the hypothesis that North American taxa are in the process of incipient speciation (Heier & Dudycha, 2009).…”
Section: Resultsmentioning
confidence: 76%
“…We first assembled short-read genomic data for 2,321 samples of D. pulex , D. pulicaria , and D. obtusa collected from North American and European ponds (Figure 1A). This includes whole genomes published elsewhere (Barnard-Kubow et al, 2022; Lynch et al, 2017; Xu et al, 2015; Ye et al, 2022), along with 93 samples reported here for the first time. We aligned samples to the European D. pulex assembly (D84A; Barnard-Kubow et al, 2022) and identified 347,200 SNPs after filtering.…”
Section: Resultsmentioning
confidence: 99%
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“…The genetic variation of mitochondrial DNA at the individual level, known as heteroplasmy, has shed valuable insights on mitogenome evolutionary and cellular processes. Heteroplasmy can result from either mutational mechanisms or a paternal leak of mtDNA (Ingman & Gyllensten, 2006;Ye et al, 2022). With older techniques, the accurate detection of heteroplasmy was difficult to achieve because NUMTs mimic polymorphism (Parakatselaki et al, 2022).…”
Section: Detecting Heteroplasmy From Hts Data and Numtsmentioning
confidence: 99%
“…The landscape and degree of recombination in mitogenomes it still a matter of debate (Thapana et al, 2022;Ye et al, 2022), with some studies on vertebrates suggesting a role in the evolution of duplicated regions. In hornbill birds, a long TR duplication with heteroplasmy showed that the two duplicated regions evolved in con-cert and likely originated from recombination (Sammler et al, 2011).…”
Section: Location Of Heteroplasmic Sites In Trs In the Cr And Genome-...mentioning
confidence: 99%