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Lee J, Willett CS. Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids. J Hered 2022; 113:171-183. [PMID: 35575078 DOI: 10.1093/jhered/esab068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.
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Affiliation(s)
- Jeeyun Lee
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher S Willett
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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HODDA M. Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept. Zootaxa 2022; 5114:290-317. [DOI: 10.11646/zootaxa.5114.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/04/2022]
Abstract
This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007). It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification. The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.
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Melvin RG, Ballard JWO. Cellular and population level processes influence the rate, accumulation and observed frequency of inherited and somatic mtDNA mutations. Mutagenesis 2017; 32:323-334. [PMID: 28521046 DOI: 10.1093/mutage/gex004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are found in all animals and have the unique feature of containing multiple copies of their own small, circular DNA genome (mtDNA). The rate and pattern of mutation accumulation in the mtDNA are influenced by molecular, cellular and population level processes. We distinguish between inherited and somatic mtDNA mutations and review evidence for the often-made assumption that mutations accumulate at a higher rate in mtDNA than in nuclear DNA (nDNA). We conclude that the whole genome mutation accumulation rate is higher for mtDNA than for nDNA but include the caveat that rates overlap considerably between the individual mtDNA- and nDNA-encoded genes. Next, we discuss the postulated causal mechanisms for the high rate of mtDNA mutation accumulation in both inheritance and in somatic cells. Perhaps unexpectedly, mtDNA is resilient to many mutagens of nDNA but is prone to errors of replication. We then consider the influence of maternal inheritance, recombination and selection on the observed accumulation pattern of inherited mtDNA mutations. Finally, we discuss environmental influences of temperature and diet on the observed frequency of inherited and somatic mtDNA mutations. We conclude that it is necessary to understand the cellular processes to fully interpret the pattern of mutations and how they influence our interpretations of evolution and disease.
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Affiliation(s)
- Richard G Melvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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Eves-van den Akker S, Lilley CJ, Reid A, Pickup J, Anderson E, Cock PJA, Blaxter M, Urwin PE, Jones JT, Blok VC. A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individual. Mol Ecol 2016; 24:5842-51. [PMID: 26607216 PMCID: PMC4981918 DOI: 10.1111/mec.13434] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/16/2015] [Accepted: 10/21/2015] [Indexed: 11/30/2022]
Abstract
Distinct populations of the potato cyst nematode (PCN) Globodera pallida exist in the UK that differ in their ability to overcome various sources of resistance. An efficient method for distinguishing between populations would enable pathogen‐informed cultivar choice in the field. Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species. We identify a region of mitochondrial DNA descriptive of three main groups of G. pallida present in the UK and adopt a metagenetic approach to the sequencing and analysis of all SASA samples simultaneously. Using this approach, we describe the distribution of G. pallida mitotypes across Scotland with field‐scale resolution. Most fields contain a single mitotype, one‐fifth contain a mix of mitotypes, and less than 3% contain all three mitotypes. Within mixed fields, we were able to quantify the relative abundance of each mitotype across an order of magnitude. Local areas within mixed fields are dominated by certain mitotypes and indicate towards a complex underlying ‘pathoscape’. Finally, we assess mitotype distribution at the level of the individual cyst and provide evidence of ‘hybrids’. This study provides a method for accurate, quantitative and high‐throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant parasite.
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Affiliation(s)
- Sebastian Eves-van den Akker
- Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Alex Reid
- Science and Advice for Scottish Agriculture, Edinburgh, EH12 9FJ, UK
| | - Jon Pickup
- Science and Advice for Scottish Agriculture, Edinburgh, EH12 9FJ, UK
| | - Eric Anderson
- Scottish Agronomy Ltd, Arlary Farm, Milnathort, Kinross, KY13 9SJ, UK
| | - Peter J A Cock
- Information and Computational Sciences Group, Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH8 9YL, UK
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.,School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
| | - Vivian C Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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Kuijper B, Lane N, Pomiankowski A. Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm? J Evol Biol 2015; 28:468-80. [PMID: 25653025 PMCID: PMC4413368 DOI: 10.1111/jeb.12582] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/05/2014] [Accepted: 01/06/2015] [Indexed: 12/13/2022]
Abstract
A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males – ’mother's curse’. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. ’reverse dominance’) are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why ’mother's curse’ is less pervasive than predicted by earlier work.
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Affiliation(s)
- B Kuijper
- CoMPLEX, Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK; Department of Genetics, Evolution and Environment, University College London, London, UK
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Besnard G, Jühling F, Chapuis É, Zedane L, Lhuillier É, Mateille T, Bellafiore S. Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. C R Biol 2014; 337:295-301. [PMID: 24841955 DOI: 10.1016/j.crvi.2014.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
Abstract
Little is known about the variations of nematode mitogenomes (mtDNA). Sequencing a complete mtDNA using a PCR approach remains a challenge due to frequent genome reorganizations and low sequence similarities between divergent nematode lineages. Here, a genome skimming approach based on HiSeq sequencing (shotgun) was used to assemble de novo the first complete mtDNA sequence of a root-knot nematode (Meloidogyne graminicola). An AT-rich genome (84.3%) of 20,030 bp was obtained with a mean sequencing depth superior to 300. Thirty-six genes were identified with a semi-automated approach. A comparison with a gene map of the M. javanica mitochondrial genome indicates that the gene order is conserved within this nematode lineage. However, deep genome rearrangements were observed when comparing with other species of the superfamily Hoplolaimoidea. Repeat elements of 111 bp and 94 bp were found in a long non-coding region of 7.5 kb, as similarly reported in M. javanica and M. hapla. This study points out the power of next generation sequencing to produce complete mitochondrial genomes, even without a reference sequence, and possibly opening new avenues for species/race identification, phylogenetics and population genetics of nematodes.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France.
| | - Frank Jühling
- University of Leipzig, Interdisciplinary Center for Bioinformatics, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Élodie Chapuis
- IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Loubab Zedane
- CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Évolution & Diversité biologique), 118, route de Narbonne, 31062 Toulouse, France
| | - Émeline Lhuillier
- INRA, GeT-PlaGe, UAR 1209 Département de génétique animale, INRA Auzeville, 31326 Castanet-Tolosan, France
| | - Thierry Mateille
- IRD, UMR 022 Centre de biologie pour la gestion des populations, campus de Baillarguet, CS30016, 34988 Montferrier-sur-Lez cedex, France
| | - Stéphane Bellafiore
- IRD, UMR186 "Résistance des plantes aux bioagresseurs", 911, avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
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Evidence of animal mtDNA recombination between divergent populations of the potato cyst nematode Globodera pallida. Genetica 2012; 140:19-29. [DOI: 10.1007/s10709-012-9651-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
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