1
|
Eto NY, Barrios-Leal DY, Manfrin MH. Introgression and Genetic Diversity Between Two Cactophilic Drosophila (Drosophila repleta group) Species: A Case Study of an Isolated Population from the Sandstone Hills in the Southeast of Brazil. NEOTROPICAL ENTOMOLOGY 2025; 54:64. [PMID: 40327225 DOI: 10.1007/s13744-025-01279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 04/08/2025] [Indexed: 05/07/2025]
Abstract
Introgressive hybridization involves the integration of genetic material from one population into another genetically distinct population. Despite its widespread occurrence in nature, the mechanisms and consequences of introgression remain poorly understood. In this study, we examine the hypothesis that the mitochondrial gene COI from Drosophila antonietae has been introgressed into the gene pool of a specific population of D. gouveai. Additionally, we extended our analysis to include other genes associated with the COX complex, such as mitochondrial (COII) and nuclear genes (CoVa, CG9603, and levy), across various populations of both species from different locations. We estimated indices of genetic diversity, constructed haplotype networks in both mitochondrial and nuclear genes, and performed selection tests to assess the evolutionary dynamics of mitochondrial genes. Our results confirm the hypothesis of a historical secondary contact between D. gouveai and D. antonietae in the region of Analândia, SP, showing asymmetric unidirectional introgression, with signs of positive selection in the mitochondrial genes.
Collapse
Affiliation(s)
- Naomi Yukie Eto
- Depto de Biologia - Faculdade de Filosofia, Ciências E Letras de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brazil
- Pós-Graduação, Depto de Genética - Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brazil
| | - Dora Yovana Barrios-Leal
- Pós-Graduação, Depto de Genética - Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brazil.
| | - Maura Helena Manfrin
- Depto de Biologia - Faculdade de Filosofia, Ciências E Letras de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brazil
- Pós-Graduação, Depto de Genética - Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brazil
| |
Collapse
|
2
|
Magalhães FDM, Oliveira EF, Garda AA, Burbrink FT, Gehara M. Genomic data support reticulate evolution in whiptail lizards from the Brazilian Caatinga. Mol Phylogenet Evol 2025; 204:108280. [PMID: 39725181 DOI: 10.1016/j.ympev.2024.108280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 12/16/2024] [Accepted: 12/21/2024] [Indexed: 12/28/2024]
Abstract
Species relationships have traditionally been represented by phylogenetic trees, but not all evolutionary histories fit into bifurcating divergence models. Introgressive hybridization challenges this assumption by sometimes [or maybe often] leading to mitochondrial introgression, wherein one species' mitochondrial genome is entirely replaced by another's (mitochondrial capture). Such processes result in mitonuclear discrepancies, complicating species delimitation and phylogenetic inference. In our study, we used ultraconserved elements (UCE) and mitogenomic data to investigate the evolutionary history of the Ameivula ocellifera complex, a group of South American whiptail lizards widely distributed in semiarid environments of the Caatinga Domain in Brazil. We examine mitonuclear discordances, assessing reticulate evolution, evaluating species limits, and testing for adaptive mitochondrial capture that could explain higher introgression in the mitochondrial genome compared to nuclear DNA. Our findings support the occurrence of an ancient reticulation event during the diversification of these lizards, driven by introgressive hybridization, leading to mitochondrial capture, and explaining mitonuclear discrepancies. Overall, we did not find clear evidence of positive selection across mitochondrial protein-coding genes suggesting adaptive mitochondrial capture of individuals with introgressed mtDNA. Thus, the genetic diversification and mitogenome evolution could be neutral, with selection against hybridization in the autosomal loci only, or even mediated by mitonuclear incompatibilities. Analyses of mtDNA genomes alongside network and species delimitation methods were crucial for identifying and validating individuals with introgressed mtDNA as a distinct species, demonstrating the potential of genome sampling, and using innovative analytical techniques for elucidating speciation processes in the presence of introgressive hybridization.
Collapse
Affiliation(s)
- Felipe de M Magalhães
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA; Programa de Pós-Graduação em Ciências Biológicas, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil.
| | - Eliana F Oliveira
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis (LAR), Departamento de Botânica e Zoologia da Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University, Newark, NJ, USA
| |
Collapse
|
3
|
Deconinck A, Madalone OF, Willett CS. Absence of heterosis for hypoxia tolerance in F1 hybrids of Tigriopus californicus. J Hered 2025; 116:149-158. [PMID: 39468759 DOI: 10.1093/jhered/esae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 10/24/2024] [Indexed: 10/30/2024] Open
Abstract
Hybridization produces a range of outcomes from advantageous to disadvantageous, and a goal of genetic research is to understand the gene interactions that generate these outcomes. Interactions between cytoplasmic elements, such as mitochondria, and the nucleus may be particularly vulnerable to accruing disadvantageous combinations as a result of their different rates of evolution. Consequently, mitonuclear incompatibilities may play an important role in hybrid outcomes even if their negative impacts could be masked for some fitness measures by heterosis in first-generation (F1) hybrids. We used Tigriopus californicus, a model system for mitonuclear incompatibilities that is also known for exhibiting heterosis in the F1 generation and outbreeding depression in later generations, to test whether heterosis or outbreeding depression would occur when mitonuclear mismatch was paired with a stress that heavily impacts mitochondrial processes-specifically, hypoxia. We generated 284 parental and 436 F1 hybrids from four population crosses (720 total) and compared parental and F1 populations for hypoxia tolerance. We observed that, on average, F1 hybrids were less likely to survive a hypoxia stress test than parental populations, although we did not detect a statistically significant trend (P = 0.246 to 0.614). This suggests that hypoxia may be a particularly intense stressor for mitonuclear coordination and hybridization outcomes vary by trait.
Collapse
Affiliation(s)
- Aimee Deconinck
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd, Chapel Hill, NC, 27599United States
| | - Olivia F Madalone
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd, Chapel Hill, NC, 27599United States
| | - Christopher S Willett
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd, Chapel Hill, NC, 27599United States
| |
Collapse
|
4
|
Cruz MA, Magalhães S, Bakırdöven M, Zélé F. Wolbachia strengthens the match between premating and early postmating isolation in spider mites. Evolution 2025; 79:203-219. [PMID: 39432669 DOI: 10.1093/evolut/qpae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 10/04/2024] [Accepted: 10/17/2024] [Indexed: 10/23/2024]
Abstract
Endosymbiotic reproductive manipulators are widely studied as sources of postzygotic isolation in arthropods, but their effect on prezygotic isolation between genetically differentiated populations has garnered less attention. We tested this using two partially isolated populations of the red and green color forms of Tetranychus urticae, either uninfected or infected with different Wolbachia strains, one inducing cytoplasmic incompatibility and the other not. We first investigated male and female preferences and found that, in absence of infection, females were not choosy, but all males preferred red-form females. Wolbachia effects were more subtle, with only the cytoplasmic incompatibility-inducing strain slightly strengthening color-form-based preferences. We then performed a double-mating experiment to test how incompatible matings affect subsequent mating behavior and offspring production as compared to compatible matings. Females mated with an incompatible male (infected and/or heterotypic) were more attractive and/or receptive to subsequent (compatible) matings, although analyses of offspring production revealed no clear benefit for this remating behavior (i.e., apparently unaltered first male sperm precedence). Finally, by computing the relative contributions of each reproductive barrier to total isolation, we showed that premating isolation matches both host-associated and Wolbachia-induced postmating isolation, suggesting that Wolbachia could contribute to reproductive isolation in this system.
Collapse
Affiliation(s)
- Miguel A Cruz
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Universidade de Lisboa, Lisboa, Portugal
| | - Sara Magalhães
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Universidade de Lisboa, Lisboa, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Murat Bakırdöven
- Institute of Environmental Sciences, Boğaziçi University, Istanbul, Turkey
| | - Flore Zélé
- Institut des Sciences de l'Évolution de Montpellier (ISEM), Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| |
Collapse
|
5
|
Jiménez AG. Is There Hybrid Vigor in Dogs? Oxidative Stress and Cytokine Concentrations in Low- To Mid-Content Wolf-Dog Hybrids. ECOLOGICAL AND EVOLUTIONARY PHYSIOLOGY 2025; 98:48-56. [PMID: 40197214 DOI: 10.1086/734630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2025]
Abstract
AbstractChanges of deleterious traits in mitochondria within hybrids of two different species are likely to be reflected across whole-animal phenotypes. Two processes linked to mitochondrial fitness are oxidative stress and inflammation. Here, plasma oxidative stress (lipid oxidative damage, total antioxidant capacity, and activities of catalase, glutathione peroxidase, and superoxide dismutase concentration) and cytokine concentrations (IL-1β, IL-6, and TNF-α) from wolf-dog hybrids of low to mid wolf content are presented and then compared with previously published values for similar-sized dogs and gray wolves. Results indicate that lipid oxidative damage and catalase activity were not significantly different across species and hybrids. Total antioxidant capacity and glutathione peroxidase were significantly lower in wolf-dog hybrids than in domestic dogs and wolves (although total antioxidant capacity significantly increased with wolf content), but superoxide dismutase concentration was higher in hybrids. Thus, it seems that a low percentage of wolf content decreases several aspects of antioxidants but without any accumulating lipid oxidative damage. Additionally, wolf-dog hybrids had higher IL-1β and IL-6 concentrations but lower TNF-α concentrations than domestic dogs. And there was a significantly positive correlation between percentage of wolf content and IL-1β. These data imply either a mitonuclear incompatibility or a nuclear-nuclear incompatibility within wolf-dog hybrids, a case that does not support heterosis.
Collapse
|
6
|
Austin LM, Amos JN, Robledo-Ruiz DA, Zhou JW, Clarke RH, Pavlova A, Sunnucks P. Random Mating in a Hybrid Zone Between Two Putative Climate-Adapted Bird Lineages With Predicted Mitonuclear Incompatibilities. Mol Ecol 2025; 34:e17612. [PMID: 39718489 DOI: 10.1111/mec.17612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/04/2024] [Accepted: 11/26/2024] [Indexed: 12/25/2024]
Abstract
Biochemical and evolutionary interactions between mitochondrial and nuclear genomes ('mitonuclear interactions') are proposed to underpin fundamental aspects of biology including evolution of sexual reproduction, adaptation and speciation. We investigated the role of pre-mating isolation in maintaining functional mitonuclear interactions in wild populations bearing diverged, putatively co-adapted mitonuclear genotypes. Two lineages of eastern yellow robin Eopsaltria australis-putatively climate-adapted to 'inland' and 'coastal' climates-differ by ~7% of mitogenome nucleotides, whereas nuclear genome differences are concentrated into a sex-linked region enriched with mitochondrial functions. Female-specific selection and male-mediated gene flow across the hybrid zone where the lineages coexist and interbreed can explain this pattern. It remains unknown whether lineage divergence is driven by intrinsic incompatibilities (particularly in females; Haldane's rule), extrinsic selection, both, or other drivers. We tested whether lineage divergence could be facilitated by non-random mate-pairing with respect to partners' mitolineage and/or mitonuclear genes encoded by the Z sex-chromosome, which differ between the lineages. We used field-, Z-linked- and mitolineage data from two locations where lineages hybridise to test whether females mate disproportionately with (1) males of their own mitolineage and/or bearing similar Z-linked variation, as might be expected if hybrids experience intrinsic incompatibilities, or (2) putatively locally-adapted males, as might be expected under environmental selection. Comparing field observations with simulations provided no evidence of non-random mating, thus drivers of observed population genetic patterns are consistent with reduced female gene flow likely acting post-mating. Future tests of female-biased mortality at different life stages and habitat selection may clarify mechanisms of selection.
Collapse
Affiliation(s)
- Lana M Austin
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - J Nevil Amos
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Energy Environment and Climate Action, Arthur Rylah Institute, Heidelberg, Victoria, Australia
| | | | - Jessica W Zhou
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Rohan H Clarke
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
7
|
Chiocchio A, de Rysky E, Carere C, Nascetti G, Bisconti R, Canestrelli D. Behavioural underpinning of mito-nuclear discordances: insights from fire salamanders. ROYAL SOCIETY OPEN SCIENCE 2024; 11:241571. [PMID: 39665091 PMCID: PMC11631422 DOI: 10.1098/rsos.241571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 11/03/2024] [Accepted: 11/04/2024] [Indexed: 12/13/2024]
Abstract
Mito-nuclear discordances across secondary contact zones have been described in a wide range of organisms. They consist of a spatial mismatch between nuclear and mitochondrial genomes in terms of location and extension of the contact zone between distinct evolutionary lineages. Despite the evolutionary and biogeographic causes of mito-nuclear discordances having been extensively investigated, we still lack a clear understanding of their phenotypic underpinnings. Here, we test the hypothesis that mtDNA variation could be associated with behavioural variation and that such association could contribute to asymmetric mitochondrial introgression across a secondary contact zone. We analysed behavioural variation across the mtDNA secondary contact zone of the fire salamander Salamandra salamandra in central Italy, which is displaced 600 km from the nuclear contact zone. We found distinct behavioural profiles in the two mitotypes co-occurring in the contact zone. The introgressed mitotype was associated with a 'slow-thorough' dispersal profile, characterized by a less active but more cautious and accurate exploration strategy. This pattern was consistent across life stages and contexts: aquatic larvae and terrestrial juveniles, spontaneous activity and response to novelty. These results support the intriguing hypothesis that personality traits associated with distinct mitotypes could contribute to differential mitochondrial introgression and the formation of biogeographic patterns of mito-nuclear discordance.
Collapse
Affiliation(s)
- Andrea Chiocchio
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viterbo, Italy
| | - Erica de Rysky
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viterbo, Italy
| | - Claudio Carere
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viterbo, Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viterbo, Italy
| | - Roberta Bisconti
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Dipartimento di Scienze Ecologiche e Biologiche, Università degli Studi della Tuscia, Viterbo, Italy
| |
Collapse
|
8
|
Nam K, Nègre N, Saldamando Benjumea CI. Two host-plant strains in the fall armyworm. INSECT SCIENCE 2024; 31:1675-1683. [PMID: 38437152 PMCID: PMC11632296 DOI: 10.1111/1744-7917.13346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
The fall armyworm (Spodoptera frugiperda) is one of the major pest insects damaging diverse crops including cotton, corn, rice, and sorghum. Fall armyworms have been identified as two morphologically indistinguishable strains, the corn strain, and the rice strain, named after their preferred host-plants. Although initially recognized as host-plant strains, there has been an ongoing debate regarding whether the corn and rice strains should be considered as such. In this article, we present arguments based on recent population genomics studies supporting that these two strains should be considered to be host-plant strains. Furthermore, host-plant adaptation appears to be a driving evolutionary force responsible for incipient speciation in the fall armyworm.
Collapse
Affiliation(s)
- Kiwoong Nam
- DGIMI, Université de Montpellier, INRAEMontpellierFrance
| | - Nicolas Nègre
- DGIMI, Université de Montpellier, INRAEMontpellierFrance
| | - Clara Ines Saldamando Benjumea
- Grupo de Biotecnología‐Vegetal UNALMED‐CIB, Laboratorio de Ecología y Evolución de Insectos 16–223Facultad de Ciencias, Departamento de Biociencias, Universidad Nacional de ColombiaMedellínColombia
| |
Collapse
|
9
|
Greenway R, De-Kayne R, Brown AP, Camarillo H, Delich C, McGowan KL, Nelson J, Arias-Rodriguez L, Kelley JL, Tobler M. Integrative analyses of convergent adaptation in sympatric extremophile fishes. Curr Biol 2024; 34:4968-4982.e7. [PMID: 39395416 DOI: 10.1016/j.cub.2024.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 07/18/2024] [Accepted: 09/11/2024] [Indexed: 10/14/2024]
Abstract
The evolution of independent lineages along replicated environmental transitions frequently results in convergent adaptation, yet the degree to which convergence is present across multiple levels of biological organization is often unclear. Additionally, inherent biases associated with shared ancestry and variation in selective regimes across geographic replicates often pose challenges for confidently identifying patterns of convergence. We investigated a system in which three species of poeciliid fishes sympatrically occur in a toxic spring rich in hydrogen sulfide (H2S) and an adjacent nonsulfidic stream to examine patterns of adaptive evolution across levels of biological organization. We found convergence in morphological and physiological traits and genome-wide patterns of gene expression among all three species. In addition, there were shared signatures of selection on genes encoding H2S toxicity targets in the mitochondrial genomes of each species. However, analyses of nuclear genomes revealed neither evidence for substantial genomic islands of divergence around genes involved in H2S toxicity and detoxification nor substantial congruence of strongly differentiated regions across population pairs. These non-convergent, heterogeneous patterns of genomic divergence may indicate that sulfide tolerance is highly polygenic, with shared allele frequency shifts present at many loci with small effects along the genome. Alternatively, H2S tolerance may involve substantial genetic redundancy, with non-convergent, lineage-specific variation at multiple loci along the genome underpinning similar changes in phenotypes and gene expression. Overall, we demonstrate variability in the extent of convergence across organizational levels and highlight the challenges of linking patterns of convergence across scales.
Collapse
Affiliation(s)
- Ryan Greenway
- Kansas State University, Division of Biology, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Rishi De-Kayne
- University of California Santa Cruz, Department of Ecology and Evolutionary Biology, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Anthony P Brown
- Washington State University, School of Biological Sciences, 301 Abelson Hall, Pullman, WA 644236, USA
| | - Henry Camarillo
- Kansas State University, Division of Biology, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Cassandra Delich
- Kansas State University, Division of Biology, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Kerry L McGowan
- Washington State University, School of Biological Sciences, 301 Abelson Hall, Pullman, WA 644236, USA
| | - Joel Nelson
- Washington State University, School of Biological Sciences, 301 Abelson Hall, Pullman, WA 644236, USA
| | - Lenin Arias-Rodriguez
- Universidad Juárez Autónoma de Tabasco, División Académica de Ciencias Biológicas, Carretera Villahermosa-Cárdenas Km. 0.5 S/N, Entronque a Bosques de Saloya, 86150 Villahermosa, Tabasco, Mexico
| | - Joanna L Kelley
- University of California Santa Cruz, Department of Ecology and Evolutionary Biology, 1156 High Street, Santa Cruz, CA 95064, USA.
| | - Michael Tobler
- University of Missouri, St. Louis, Department of Biology, 1 University Boulevard, St. Louis, MO 63121, USA; University of Missouri, St. Louis, Whitney R. Harris World Ecology Center, 1 University Boulevard, St. Louis, MO 63121, USA; Saint Louis Zoo, WildCare Institute, 1 Government Drive, St. Louis, MO 63110, USA.
| |
Collapse
|
10
|
Smith CH, Mejia-Trujillo R, Havird JC. Mitonuclear compatibility is maintained despite relaxed selection on male mitochondrial DNA in bivalves with doubly uniparental inheritance. Evolution 2024; 78:1790-1803. [PMID: 38995057 PMCID: PMC11519007 DOI: 10.1093/evolut/qpae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 06/03/2024] [Accepted: 07/11/2024] [Indexed: 07/13/2024]
Abstract
Mitonuclear coevolution is common in eukaryotes, but bivalve lineages that have doubly uniparental inheritance (DUI) of mitochondria may be an interesting example. In this system, females transmit mtDNA (F mtDNA) to all offspring, while males transmit a different mtDNA (M mtDNA) solely to their sons. Molecular evolution and functional data suggest oxidative phosphorylation (OXPHOS) genes encoded in M mtDNA evolve under relaxed selection due to their function being limited to sperm only (vs. all other tissues for F mtDNA). This has led to the hypothesis that mitonuclear coevolution is less important for M mtDNA. Here, we use comparative phylogenetics, transcriptomics, and proteomics to understand mitonuclear interactions in DUI bivalves. We found nuclear OXPHOS proteins coevolve and maintain compatibility similarly with both F and M mtDNA OXPHOS proteins. Mitochondrial recombination did not influence mitonuclear compatibility and nuclear-encoded OXPHOS genes were not upregulated in tissues with M mtDNA to offset dysfunction. Our results support that selection maintains mitonuclear compatibility with F and M mtDNA despite relaxed selection on M mtDNA. Strict sperm transmission, lower effective population size, and higher mutation rates may explain the evolution of M mtDNA. Our study highlights that mitonuclear coevolution and compatibility may be broad features of eukaryotes.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Raquel Mejia-Trujillo
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
11
|
Thoral E, Dawson NJ, Bettinazzi S, Rodríguez E. An evolving roadmap: using mitochondrial physiology to help guide conservation efforts. CONSERVATION PHYSIOLOGY 2024; 12:coae063. [PMID: 39252884 PMCID: PMC11381570 DOI: 10.1093/conphys/coae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/11/2024]
Abstract
The crucial role of aerobic energy production in sustaining eukaryotic life positions mitochondrial processes as key determinants of an animal's ability to withstand unpredictable environments. The advent of new techniques facilitating the measurement of mitochondrial function offers an increasingly promising tool for conservation approaches. Herein, we synthesize the current knowledge on the links between mitochondrial bioenergetics, ecophysiology and local adaptation, expanding them to the wider conservation physiology field. We discuss recent findings linking cellular bioenergetics to whole-animal fitness, in the current context of climate change. We summarize topics, questions, methods, pitfalls and caveats to help provide a comprehensive roadmap for studying mitochondria from a conservation perspective. Our overall aim is to help guide conservation in natural populations, outlining the methods and techniques that could be most useful to assess mitochondrial function in the field.
Collapse
Affiliation(s)
- Elisa Thoral
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
| | - Neal J Dawson
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Garscube Campus, Bearsden Road, Glasgow, G61 1QH , UK
| | - Stefano Bettinazzi
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, 99-105 Gower Street, WC1E 6BT, London, UK
| | - Enrique Rodríguez
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, 99-105 Gower Street, WC1E 6BT, London, UK
| |
Collapse
|
12
|
Li H, Liang X, Peng Y, Liu Z, Zhang L, Wang P, Jin M, Wilson K, Garvin MR, Wu K, Xiao Y. Novel Mito-Nuclear Combinations Facilitate the Global Invasion of a Major Agricultural Crop Pest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305353. [PMID: 38965806 PMCID: PMC11425838 DOI: 10.1002/advs.202305353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 04/24/2024] [Indexed: 07/06/2024]
Abstract
A fundamental understanding of the underlying mechanisms involved in biological invasions is crucial to developing effective risk assessment and control measures against invasive species. The fall armyworm (FAW), Spodoptera frugiperda, is a highly invasive pest that has rapidly spread from its native Americas into much of the Eastern Hemisphere, with a highly homogeneous nuclear genetic background. However, the exact mechanism behind its rapid introduction and propagation remains unclear. Here, a systematic investigation is conducted into the population dynamics of FAW in China from 2019 to 2021 and found that FAW individuals carrying "rice" mitochondria (FAW-mR) are more prevalent (>98%) than that with "corn" mitochondria (FAW-mC) at the initial stage of the invasion and in newly-occupied non-overwintering areas. Further fitness experiments show that the two hybrid-strains of FAW exhibit different adaptions in the new environment in China, and this may have been facilitated by amino acid changes in mitochondrial-encoded proteins. FAW-mR used increases energy metabolism, faster wing-beat frequencies, and lower wing loadings to drive greater flight performance and subsequent rapid colonization of new habitats. In contrast, FAW-mC individuals adapt with more relaxed mitochondria and shuttle energetics into maternal investment, observed as faster development rate and higher fecundity. The presence of two different mitochondria types within FAW has the potential to significantly expand the range of damage and enhance competitive advantage. Overall, the study describes a novel invasion mechanism displayed by the FAW population that facilitates its expansion and establishment in new environments.
Collapse
Affiliation(s)
- Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xinyue Liang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhenxing Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Ping Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Minghui Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kenneth Wilson
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Michael R Garvin
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37830, USA
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| |
Collapse
|
13
|
Li N, Flanagan BA, Edmands S. The role of mitochondria in sex- and age-specific gene expression in a species without sex chromosomes. Proc Natl Acad Sci U S A 2024; 121:e2321267121. [PMID: 38838014 PMCID: PMC11181141 DOI: 10.1073/pnas.2321267121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 05/13/2024] [Indexed: 06/07/2024] Open
Abstract
Mitochondria perform an array of functions, many of which involve interactions with gene products encoded by the nucleus. These mitochondrial functions, particularly those involving energy production, can be expected to differ between sexes and across ages. Here, we measured mitochondrial effects on sex- and age-specific gene expression in parental and reciprocal F1 hybrids between allopatric populations of Tigriopus californicus with over 20% mitochondrial DNA divergence. Because the species lacks sex chromosomes, sex-biased mitochondrial effects are not confounded by the effects of sex chromosomes. Results revealed pervasive sex differences in mitochondrial effects, including effects on energetics and aging involving nuclear interactions throughout the genome. Using single-individual RNA sequencing, sex differences were found to explain more than 80% of the variance in gene expression. Males had higher expression of mitochondrial genes and mitochondrially targeted proteins (MTPs) involved in oxidative phosphorylation (OXPHOS), while females had elevated expression of non-OXPHOS MTPs, indicating strongly sex-dimorphic energy metabolism at the whole organism level. Comparison of reciprocal F1 hybrids allowed insights into the nature of mito-nuclear interactions, showing both mitochondrial effects on nuclear expression, and nuclear effects on mitochondrial expression. While based on a small set of crosses, sex-specific increases in mitochondrial expression with age were associated with longer life. Network analyses identified nuclear components of strong mito-nuclear interactions and found them to be sexually dimorphic. These results highlight the profound impact of mitochondria and mito-nuclear interactions on sex- and age-specific gene expression.
Collapse
Affiliation(s)
- Ning Li
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90089
| | - Ben A. Flanagan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90089
| | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA90089
| |
Collapse
|
14
|
Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024; 54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.
Collapse
Affiliation(s)
- Dong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Ivan Jakovlić
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fei Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Institute of Aquatic Sciences, Tibet Academy of Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China
| | - Chuan-Yu Xiang
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qunzong Gusang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Sonam Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Shenggui Xue
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Wen-Jin Zhu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Zhenxin Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Jihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
15
|
Crino OL, Head ML, Jennions MD, Noble DWA. Mitochondrial function and sexual selection: can physiology resolve the 'lek paradox'? J Exp Biol 2024; 227:jeb245569. [PMID: 38206324 DOI: 10.1242/jeb.245569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Across many taxa, males use elaborate ornaments or complex displays to attract potential mates. Such sexually selected traits are thought to signal important aspects of male 'quality'. Female mating preferences based on sexual traits are thought to have evolved because choosy females gain direct benefits that enhance their lifetime reproductive success (e.g. greater access to food) and/or indirect benefits because high-quality males contribute genes that increase offspring fitness. However, it is difficult to explain the persistence of female preferences when males only provide genetic benefits, because female preferences should erode the heritable genetic variation in fitness that sexually selected traits signal. This 'paradox of the lek' has puzzled evolutionary biologists for decades, and inspired many hypotheses to explain how heritable variation in sexually selected traits is maintained. Here, we discuss how factors that affect mitochondrial function can maintain variation in sexually selected traits despite strong female preferences. We discuss how mitochondrial function can influence the expression of sexually selected traits, and we describe empirical studies that link the expression of sexually selected traits to mitochondrial function. We explain how mothers can affect mitochondrial function in their offspring by (a) influencing their developmental environment through maternal effects and (b) choosing a mate to increase the compatibility of mitochondrial and nuclear genes (i.e. the 'mitonuclear compatibility model of sexual selection'). Finally, we discuss how incorporating mitochondrial function into models of sexual selection might help to resolve the paradox of the lek, and we suggest avenues for future research.
Collapse
Affiliation(s)
- Ondi L Crino
- School of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Megan L Head
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Michael D Jennions
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Centre, 10 Marais Street, Stellenbosch 7600, South Africa
| | - Daniel W A Noble
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| |
Collapse
|
16
|
Li N, Flanagan BA, Edmands S. The role of mitochondria in sex- and age-specific gene expression in a species without sex chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570893. [PMID: 38106076 PMCID: PMC10723445 DOI: 10.1101/2023.12.08.570893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mitochondria perform an array of functions, many of which involve interactions with gene products encoded by the nucleus. These mitochondrial functions, particularly those involving energy production, can be expected to differ between sexes and across ages. Here we measured mitochondrial effects on sex- and age-specific gene expression in parental and reciprocal F1 hybrids between allopatric populations of Tigriopus californicus with over 20% mitochondrial DNA divergence. Because the species lacks sex chromosomes, sex-biased mitochondrial effects are not confounded by the effects of sex chromosomes. Using single-individual RNA sequencing, sex differences were found to explain more than 80% of the variance in gene expression. Males had higher expression of mitochondrial genes and mitochondrially targeted proteins (MTPs) involved in oxidative phosphorylation (OXPHOS), while females had elevated expression of non-OXPHOS MTPs, indicating strongly sex-dimorphic energy metabolism at the whole organism level. Comparison of reciprocal F1 hybrids allowed insights into the nature of mito-nuclear interactions, showing both mitochondrial effects on nuclear expression, as well as nuclear effects on mitochondrial expression. Across both sexes, increases in mitochondrial expression with age were associated with longer life. Network analyses identified nuclear components of strong mito-nuclear interactions, and found them to be sexually dimorphic. These results highlight the profound impact of mitochondria and mito-nuclear interactions on sex- and age-specific gene expression.
Collapse
Affiliation(s)
- Ning Li
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | | | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| |
Collapse
|
17
|
Sun KK, Ding Y, Chen L, Sun JT. A Comparative Analysis of Selection Pressures Suffered by Mitochondrial Genomes in Two Planthopper Species with Divergent Climate Distributions. Int J Mol Sci 2023; 24:16847. [PMID: 38069176 PMCID: PMC10706623 DOI: 10.3390/ijms242316847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been widely used as a valuable tool in studies related to evolution and population genetics, under the implicit assumption of neutral evolution. However, recent studies suggest that natural selection also plays a significant role in shaping mitochondrial genome evolution, although the specific driving forces remain elusive. In this study, we aimed to investigate whether and how climate influences mitochondrial genome evolution by comparing the selection pressures acting on mitochondrial genomes between two rice planthoppers, Sogatella furcifera (Horváth) and Laodelphax striatellus (Fallén), which have different climate distributions. We employed the dN/dS method, MK test and Tajima's D tests for our analysis. Our results showed that the mitochondrial genomes of the two species appear to undergo predominantly purifying selection, consistent with the nearly neutral evolution model. However, we observed varied degrees of purifying selection among the 13 protein-coding genes. Notably, ND1, ND2, ND6, COIII, and ATP8 exhibited significantly stronger purifying selection and greater divergence between the two species compared to the other genes. Additionally, we observed relatively stronger purifying selection in the mitochondrial genomes of S. furcifera compared to L. striatellus. This difference could be attributed to varying metabolic requirements arising from distinct habitats or other factors that are unclear here. Furthermore, we speculate that mito-nuclear epistatic interactions may play a role in maintaining nonsynonymous polymorphisms, particularly for COI and COII. Overall, our results shed some light on the influence of climate on mitochondrial genome evolution.
Collapse
Affiliation(s)
| | | | | | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing 210095, China; (K.-K.S.); (Y.D.)
| |
Collapse
|
18
|
Healy TM, Burton RS. Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence. Evolution 2023; 77:2100-2108. [PMID: 37407024 DOI: 10.1093/evolut/qpad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.
Collapse
Affiliation(s)
- Timothy M Healy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
| |
Collapse
|
19
|
Bracewell RR, Stillman JH, Dahlhoff EP, Smeds E, Chatla K, Bachtrog D, Williams C, Rank NE. A chromosome-scale genome assembly and evaluation of mtDNA variation in the willow leaf beetle Chrysomela aeneicollis. G3 (BETHESDA, MD.) 2023; 13:jkad106. [PMID: 37178174 PMCID: PMC10320752 DOI: 10.1093/g3journal/jkad106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/08/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
The leaf beetle Chrysomela aeneicollis has a broad geographic range across Western North America but is restricted to cool habitats at high elevations along the west coast. Central California populations occur only at high altitudes (2,700-3,500 m) where they are limited by reduced oxygen supply and recent drought conditions that are associated with climate change. Here, we report a chromosome-scale genome assembly alongside a complete mitochondrial genome and characterize differences among mitochondrial genomes along a latitudinal gradient over which beetles show substantial population structure and adaptation to fluctuating temperatures. Our scaffolded genome assembly consists of 21 linkage groups; one of which we identified as the X chromosome based on female/male whole genome sequencing coverage and orthology with Tribolium castaneum. We identified repetitive sequences in the genome and found them to be broadly distributed across all linkage groups. Using a reference transcriptome, we annotated a total of 12,586 protein-coding genes. We also describe differences in putative secondary structures of mitochondrial RNA molecules, which may generate functional differences important in adaptation to harsh abiotic conditions. We document substitutions at mitochondrial tRNA molecules and substitutions and insertions in the 16S rRNA region that could affect intermolecular interactions with products from the nuclear genome. This first chromosome-level reference genome will enable genomic research in this important model organism for understanding the biological impacts of climate change on montane insects.
Collapse
Affiliation(s)
- Ryan R Bracewell
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathon H Stillman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | | | - Elliott Smeds
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Caroline Williams
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan E Rank
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| |
Collapse
|
20
|
Smith CH, Pinto BJ, Kirkpatrick M, Hillis DM, Pfeiffer JM, Havird JC. A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance. J Hered 2023; 114:199-206. [PMID: 36897956 PMCID: PMC10212130 DOI: 10.1093/jhered/esad004] [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: 10/22/2022] [Accepted: 01/19/2023] [Indexed: 03/12/2023] Open
Abstract
In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Brendan J Pinto
- Center for Evolutionary Medicine & Public Health, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - David M Hillis
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - John M Pfeiffer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| |
Collapse
|
21
|
Sloan DB, DeTar RA, Warren JM. Aminoacyl-tRNA Synthetase Evolution within the Dynamic Tripartite Translation System of Plant Cells. Genome Biol Evol 2023; 15:evad050. [PMID: 36951086 PMCID: PMC10098043 DOI: 10.1093/gbe/evad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/24/2023] Open
Abstract
Eukaryotes maintain separate protein translation systems for nuclear and organellar genes, including distinct sets of tRNAs and aminoacyl-tRNA synthetases (aaRSs). In animals, mitochondrial-targeted aaRSs are expressed at lower levels and are less conserved in sequence than cytosolic aaRSs involved in translation of nuclear mRNAs, likely reflecting lower translational demands in mitochondria. In plants, translation is further complicated by the presence of plastids, which share most aaRSs with mitochondria. In addition, plant mitochondrial tRNA pools have a dynamic history of gene loss and functional replacement by tRNAs from other compartments. To investigate the consequences of these distinctive features of translation in plants, we analyzed sequence evolution in angiosperm aaRSs. In contrast to previously studied eukaryotic systems, we found that plant organellar and cytosolic aaRSs exhibit only a small difference in expression levels, and organellar aaRSs are slightly more conserved than cytosolic aaRSs. We hypothesize that these patterns result from high translational demands associated with photosynthesis in mature chloroplasts. We also investigated aaRS evolution in Sileneae, an angiosperm lineage with extensive mitochondrial tRNA replacement and aaRS retargeting. We predicted positive selection for changes in aaRS sequence resulting from these recent changes in subcellular localization and tRNA substrates but found little evidence for accelerated sequence divergence. Overall, the complex tripartite translation system in plant cells appears to have imposed more constraints on the long-term evolutionary rates of organellar aaRSs compared with other eukaryotic lineages, and plant aaRS protein sequences appear largely robust to more recent perturbations in subcellular localization and tRNA interactions.
Collapse
Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins
| | - Rachael A DeTar
- Department of Biology, Colorado State University, Fort Collins
| | - Jessica M Warren
- Center for Mechanisms of Evolution, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe
| |
Collapse
|
22
|
Kyrgiafini MA, Giannoulis T, Moutou KA, Mamuris Z. Investigating the Impact of a Curse: Diseases, Population Isolation, Evolution and the Mother's Curse. Genes (Basel) 2022; 13:2151. [PMID: 36421825 PMCID: PMC9690142 DOI: 10.3390/genes13112151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 09/08/2024] Open
Abstract
The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother's Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother's Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother's Curse.
Collapse
Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| |
Collapse
|
23
|
Weaver RJ, Rabinowitz S, Thueson K, Havird JC. Genomic Signatures of Mitonuclear Coevolution in Mammals. Mol Biol Evol 2022; 39:6775223. [PMID: 36288802 PMCID: PMC9641969 DOI: 10.1093/molbev/msac233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) and nuclear-encoded proteins are integrated in aerobic respiration, requiring co-functionality among gene products from fundamentally different genomes. Different evolutionary rates, inheritance mechanisms, and selection pressures set the stage for incompatibilities between interacting products of the two genomes. The mitonuclear coevolution hypothesis posits that incompatibilities may be avoided if evolution in one genome selects for complementary changes in interacting genes encoded by the other genome. Nuclear compensation, in which deleterious mtDNA changes are offset by compensatory nuclear changes, is often invoked as the primary mechanism for mitonuclear coevolution. Yet, direct evidence supporting nuclear compensation is rare. Here, we used data from 58 mammalian species representing eight orders to show strong correlations between evolutionary rates of mt and nuclear-encoded mt-targeted (N-mt) proteins, but not between mt and non-mt-targeted nuclear proteins, providing strong support for mitonuclear coevolution across mammals. N-mt genes with direct mt interactions also showed the strongest correlations. Although most N-mt genes had elevated dN/dS ratios compared to mt genes (as predicted under nuclear compensation), N-mt sites in close contact with mt proteins were not overrepresented for signs of positive selection compared to noncontact N-mt sites (contrary to predictions of nuclear compensation). Furthermore, temporal patterns of N-mt and mt amino acid substitutions did not support predictions of nuclear compensation, even in positively selected, functionally important residues with direct mitonuclear contacts. Overall, our results strongly support mitonuclear coevolution across ∼170 million years of mammalian evolution but fail to support nuclear compensation as the major mode of mitonuclear coevolution.
Collapse
Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA.,Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA
| | | | - Kiley Thueson
- Department of Integrative Biology, University of Texas, Austin, TX
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX
| |
Collapse
|
24
|
Kvistad L, Falk S, Austin L. Widespread genomic signatures of reproductive isolation and sex-specific selection in the Eastern Yellow Robin, Eopsaltria australis. G3 GENES|GENOMES|GENETICS 2022; 12:6605223. [PMID: 35686912 PMCID: PMC9438485 DOI: 10.1093/g3journal/jkac145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/31/2022] [Indexed: 11/16/2022]
Abstract
How new species evolve is one of the most fundamental questions in biology. Population divergence, which may lead to speciation, may be occurring in the Eastern Yellow Robin, a common passerine that lives along the eastern coast of Australia. This species is composed of 2 parapatric lineages that have highly divergent mitochondrial DNA; however, similar levels of divergence have not been observed in the nuclear genome. Here we re-examine the nuclear genomes of these mitolineages to test potential mechanisms underlying the discordance between nuclear and mitochondrial divergence. We find that nuclear admixture occurs in a narrow hybrid zone, although the majority of markers across the genome show evidence of reproductive isolation between populations of opposing mitolineages. There is an 8 MB section of a previously identified putative neo-sex chromosome that is highly diverged between allopatric but not parapatric populations, which may be the result of a chromosomal inversion. The neo-sex chromosomal nature of this region, as well as the geographic patterns in which it exhibits divergence, suggest it is unlikely to be contributing to reproductive isolation through mitonuclear incompatibilities as reported in earlier studies. In addition, there are sex differences in the number of markers that are differentiated between populations of opposite mitolineages, with greater differentiation occurring in females, which are heterozygous, than males. These results suggest that, despite the absence of previously observed assortative mating, mitolineages of Eastern Yellow Robin experience at least some postzygotic isolation from each other, in a pattern consistent with Haldane’s Rule.
Collapse
Affiliation(s)
- Lynna Kvistad
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
| | - Stephanie Falk
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
- Deep Sequencing Facility, Max Planck Institute of Immunobiology and Epigenetics , Freiburg D-79108, Germany
| | - Lana Austin
- Biological Sciences, Monash University , Clayton, VIC 3800, Australia
| |
Collapse
|
25
|
Visinoni F, Delneri D. Mitonuclear interplay in yeast: from speciation to phenotypic adaptation. Curr Opin Genet Dev 2022; 76:101957. [PMID: 35870233 DOI: 10.1016/j.gde.2022.101957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 11/03/2022]
Abstract
Saccharomyces yeasts have evolved into an important model system to study mitonuclear incompatibilities, thanks to recent advances in the field of sequencing, yeast hybridisation and multigenerational breeding. Yeast hybrids contain two homologous proteomes but retain only one type of mitochondria allowing studies on the effect of mitochondria on phenotype and gene expression. Here, we discuss the recent developments in the growing field of yeast mitogenomics spanning from the impact that this organelle has in shaping yeast fitness and genome evolution to the dissection of molecular determinants of mitonuclear incompatibilities. Applying the state-of-the-art genetic tools to a broader range of natural yeast species from different environments will help progress the field and untap the mitochondrial potential in strain development.
Collapse
Affiliation(s)
- Federico Visinoni
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Daniela Delneri
- Manchester Institute of Biotechnology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
26
|
Crino OL, Falk S, Katsis AC, Kraft FLOH, Buchanan KL. Mitochondria as the powerhouses of sexual selection: Testing mechanistic links between development, cellular respiration, and bird song. Horm Behav 2022; 142:105184. [PMID: 35596967 DOI: 10.1016/j.yhbeh.2022.105184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/04/2022]
Abstract
The developmental environment can affect the expression of sexually selected traits in adulthood. The physiological mechanisms that modulate such effects remain a matter of intense debate. Here, we test the role of the developmental environment in shaping adult mitochondrial function and link mitochondrial function to expression of a sexually selected trait in males (bird song). We exposed male zebra finches (Taeniopygia guttata) to corticosterone (CORT) treatment during development. After males reached adulthood, we quantified mitochondrial function from whole red blood cells and measured baseline CORT and testosterone levels, body condition/composition, and song structure. CORT-treated males had mitochondria that were less efficient (FCRL/R) and used a lower proportion of maximum capacity (FCRR/ETS) than control males. Additionally, CORT-treated males had higher baseline levels of CORT as adults compared to control males. Using structural equation modelling, we found that the effects of CORT treatment during development on adult mitochondrial function were indirect and modulated by baseline CORT levels, which are programmed by CORT treatment during development. Developmental treatment also had an indirect effect on song peak frequency. Males treated with CORT during development sang songs with higher peak frequency than control males, but this effect was modulated through increased CORT levels and by a decrease in FCRR/ETS. CORT-treated males had smaller tarsi compared to control males; however, there were no associations between body size and measures of song frequency. Here, we provide the first evidence supporting links between the developmental environment, mitochondrial function, and the expression of a sexually selected trait (bird song).
Collapse
Affiliation(s)
- Ondi L Crino
- Research School of Biology, Australian National University, Canberra, ACT, Australia; Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.
| | - Steph Falk
- School of Biological Science Monash University, Melbourne, VIC, Australia; Institute of Immunology and Epigenetics, Max Planck Institute, Baden-Württemberg, Germany
| | - Andrew C Katsis
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Fanny-Linn O H Kraft
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia; Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Katherine L Buchanan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| |
Collapse
|
27
|
Noll D, Leon F, Brandt D, Pistorius P, Le Bohec C, Bonadonna F, Trathan PN, Barbosa A, Rey AR, Dantas GPM, Bowie RCK, Poulin E, Vianna JA. Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation. Sci Rep 2022; 12:3767. [PMID: 35260629 PMCID: PMC8904570 DOI: 10.1038/s41598-022-07562-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.
Collapse
Affiliation(s)
- D Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - F Leon
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - D Brandt
- Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - P Pistorius
- Department of Zoology, 11DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Nelson Mandela University, Port Elizabeth, South Africa
| | - C Le Bohec
- CNRS, IPHC UMR 7178, Université de Strasbourg, 67000, Strasbourg, France.,Département de Biologie Polaire, Centre Scientifique de Monaco, 98000, Monaco City, Monaco
| | - F Bonadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier Cedex 5, France
| | | | - A Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - A Raya Rey
- Centro Austral de Investigaciones Científicas - Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Argentina.,Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - G P M Dantas
- PPG in Vertebrate Biology, Pontificia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - R C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - E Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - J A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile. .,Fondo de Desarrollo de Áreas Prioritarias (FONDAP), Center for Genome Regulation (CRG), Santiago, Chile.
| |
Collapse
|
28
|
Meza‐Lázaro RN, Peña‐Carrillo KI, Poteaux C, Lorenzi MC, Wetterer JK, Zaldívar‐Riverón A. Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex. Ecol Evol 2022; 12:e8704. [PMID: 35342602 PMCID: PMC8928884 DOI: 10.1002/ece3.8704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
Geographic separation that leads to the evolution of reproductive isolation between populations generally is considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due to phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence, and mitonuclear conflict. Here, we performed an integrative study based on two genome-wide techniques (3RAD and ultraconserved elements) coupled with cuticular hydrocarbon (CHC) and mitochondrial (mt) DNA sequence data, to assess the species limits within the Ectatomma ruidum species complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy (i.e., presence of multiple mtDNA variants in an individual) has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex: two widely distributed across the Neotropics, and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, CHC differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.
Collapse
Affiliation(s)
- Rubi N. Meza‐Lázaro
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Kenzy I. Peña‐Carrillo
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
- INIFAPCampo Experimental General TeránGeneral TeránMexico
| | - Chantal Poteaux
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - Maria Cristina Lorenzi
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - James K. Wetterer
- Harriet L. Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alejandro Zaldívar‐Riverón
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| |
Collapse
|
29
|
Vázquez-Miranda H, Zink RM, Pinto BJ. Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence. Mol Phylogenet Evol 2022; 171:107466. [DOI: 10.1016/j.ympev.2022.107466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/22/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
|
30
|
Kwon T, Kim K, Caetano-Anolles K, Sung S, Cho S, Jeong C, Hanotte O, Kim H. Mitonuclear incompatibility as a hidden driver behind the genome ancestry of African admixed cattle. BMC Biol 2022; 20:20. [PMID: 35039029 PMCID: PMC8764764 DOI: 10.1186/s12915-021-01206-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Africa is an important watershed in the genetic history of domestic cattle, as two lineages of modern cattle, Bos taurus and B. indicus, form distinct admixed cattle populations. Despite the predominant B. indicus nuclear ancestry of African admixed cattle, B. indicus mitochondria have not been found on the continent. This discrepancy between the mitochondrial and nuclear genomes has been previously hypothesized to be driven by male-biased introgression of Asian B. indicus into ancestral African B. taurus. Given that this hypothesis mandates extreme demographic assumptions relying on random genetic drift, we propose a novel hypothesis of selection induced by mitonuclear incompatibility and assess these hypotheses with regard to the current genomic status of African admixed cattle. Results By analyzing 494 mitochondrial and 235 nuclear genome sequences, we first confirmed the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle: the absence of B. indicus mitochondria and the predominant B. indicus autosomal ancestry. We applied approximate Bayesian computation (ABC) to assess the posterior probabilities of two selection hypotheses given this observation. The results of ABC indicated that the model assuming both male-biased B. indicus introgression and selection induced by mitonuclear incompatibility explains the current genomic discrepancy most accurately. Subsequently, we identified selection signatures at autosomal loci interacting with mitochondria that are responsible for integrity of the cellular respiration system. By contrast with B. indicus-enriched genome ancestry of African admixed cattle, local ancestries at these selection signatures were enriched with B. taurus alleles, concurring with the key expectation of selection induced by mitonuclear incompatibility. Conclusions Our findings support the current genome status of African admixed cattle as a potential outcome of male-biased B. indicus introgression, where mitonuclear incompatibility exerted selection pressure against B. indicus mitochondria. This study provides a novel perspective on African cattle demography and supports the role of mitonuclear incompatibility in the hybridization of mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01206-x.
Collapse
Affiliation(s)
- Taehyung Kwon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,eGnome, Inc, Seoul, South Korea
| | | | | | | | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, UK. .,LiveGene, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia. .,The Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, The University of Edinburgh, Edinburgh, UK.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea. .,eGnome, Inc, Seoul, South Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea.
| |
Collapse
|
31
|
Lubawy J, Chowański S, Adamski Z, Słocińska M. Mitochondria as a target and central hub of energy division during cold stress in insects. Front Zool 2022; 19:1. [PMID: 34991650 PMCID: PMC8740437 DOI: 10.1186/s12983-021-00448-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
Temperature stress is one of the crucial factors determining geographical distribution of insect species. Most of them are active in moderate temperatures, however some are capable of surviving in extremely high as well as low temperatures, including freezing. The tolerance of cold stress is a result of various adaptation strategies, among others the mitochondria are an important player. They supply cells with the most prominent energy carrier—ATP, needed for their life processes, but also take part in many other processes like growth, aging, protection against stress injuries or cell death. Under cold stress, the mitochondria activity changes in various manner, partially to minimize the damages caused by the cold stress, partially because of the decline in mitochondrial homeostasis by chill injuries. In the response to low temperature, modifications in mitochondrial gene expression, mtDNA amount or phosphorylation efficiency can be observed. So far study also showed an increase or decrease in mitochondria number, their shape and mitochondrial membrane permeability. Some of the changes are a trigger for apoptosis induced via mitochondrial pathway, that protects the whole organism against chill injuries occurring on the cellular level. In many cases, the observed modifications are not unequivocal and depend strongly on many factors including cold acclimation, duration and severity of cold stress or environmental conditions. In the presented article, we summarize the current knowledge about insect response to cold stress focusing on the role of mitochondria in that process considering differences in results obtained in different experimental conditions, as well as depending on insect species. These differentiated observations clearly indicate that it is still much to explore. ![]()
Collapse
Affiliation(s)
- Jan Lubawy
- Department of Animal Physiology and Developmental Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.
| | - Szymon Chowański
- Department of Animal Physiology and Developmental Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zbigniew Adamski
- Department of Animal Physiology and Developmental Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.,Laboratory of Electron and Confocal Microscopy, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Małgorzata Słocińska
- Department of Animal Physiology and Developmental Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| |
Collapse
|
32
|
Sato Y, Fujiwara S, Egas M, Matsuda T, Gotoh T. Patterns of reproductive isolation in a haplodiploid mite, Amphitetranychus viennensis: prezygotic isolation, hybrid inviability and hybrid sterility. BMC Ecol Evol 2021; 21:177. [PMID: 34551724 PMCID: PMC8459536 DOI: 10.1186/s12862-021-01896-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 08/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Evolution of reproductive isolation is an important process, generating biodiversity and driving speciation. To better understand this process, it is necessary to investigate factors underlying reproductive isolation through various approaches but also in various taxa. Previous studies, mainly focusing on diploid animals, supported the prevalent view that reproductive barriers evolve gradually as a by-product of genetic changes accumulated by natural selection by showing a positive relationship between the degree of reproductive isolation and genetic distance. Haplodiploid animals are expected to generate additional insight into speciation, but few studies investigated the prevalent view in haplodiploid animals. In this study, we investigate whether the relationship also holds in a haplodiploid spider mite, Amphitetranychus viennensis (Zacher). RESULTS We sampled seven populations of the mite in the Palaearctic region, measured their genetic distance (mtDNA) and carried out cross experiments with all combinations. We analyzed how lack of fertilization rate (as measure of prezygotic isolation) as well as hybrid inviability and hybrid sterility (as measures of postzygotic isolation) varies with genetic distance. We found that the degree of reproductive isolation varies among cross combinations, and that all three measures of reproductive isolation have a positive relationship with genetic distance. Based on the mtDNA marker, lack of fertilization rate, hybrid female inviability and hybrid female sterility were estimated to be nearly complete (99.0-99.9% barrier) at genetic distances of 0.475-0.657, 0.150-0.209 and 0.145-0.210, respectively. Besides, we found asymmetries in reproductive isolation. CONCLUSIONS The prevalent view on the evolution of reproductive barriers is supported in the haplodiploid spider mite we studied here. According to the estimated minimum genetic distance for total reproductive isolation in parent population crosses in this study and previous work, a genetic distance of 0.15-0.21 in mtDNA (COI) appears required for speciation in spider mites. Variations and asymmetries in the degree of reproductive isolation highlight the importance of reinforcement of prezygotic reproductive isolation through incompatibility and the importance of cytonuclear interactions for reproductive isolation in haplodiploid spider mites.
Collapse
Affiliation(s)
- Yukie Sato
- Faculty of Life and Environmental Science/Mountain Science Center, University of Tsukuba, Ibaraki, 305-8577, Japan
| | - Satoshi Fujiwara
- Laboratory of Applied Entomology and Zoology, Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, 300-0393, Japan
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Tomoko Matsuda
- Laboratory of Applied Entomology and Zoology, Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, 300-0393, Japan.,Nihon BioData Corporation, Kawasaki, Kanagawa, 213-0012, Japan
| | - Tetsuo Gotoh
- Laboratory of Applied Entomology and Zoology, Faculty of Agriculture, Ibaraki University, Ami, Ibaraki, 300-0393, Japan. .,Faculty of Economics, Ryutsu Keizai University, Ryugasaki, Ibaraki, 301-8555, Japan.
| |
Collapse
|
33
|
Dégletagne C, Abele D, Glöckner G, Alric B, Gruber H, Held C. Presence of male mitochondria in somatic tissues and their functional importance at the whole animal level in the marine bivalve Arctica islandica. Commun Biol 2021; 4:1104. [PMID: 34545198 PMCID: PMC8452683 DOI: 10.1038/s42003-021-02593-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/16/2021] [Indexed: 02/08/2023] Open
Abstract
Metazoans normally possess a single lineage of mitochondria inherited from the mother (♀-type mitochondria) while paternal mitochondria are absent or eliminated in fertilized eggs. In doubly uniparental inheritance (DUI), which is specific to the bivalve clade including the ocean quahog, Arctica islandica, ♂-type mitochondria are retained in male gonads and, in a few species, small proportions of ♂-type mitochondria co-exist with ♀-type in somatic tissues. To the best of our knowledge, we report, for the first time in metazoan, the natural occurrence of male and female individuals with exclusively ♂-type mitochondria in somatic tissues of the bivalve A. islandica. Mitochondrial genomes differ by ~5.5% at DNA sequence level. Exclusive presence of ♂-type mitochondria affects mitochondrial complexes partially encoded by mitochondrial genes and leads to a sharp drop in respiratory capacity. Through a combination of whole mitochondrial genome sequencing and molecular assays (gene presence and expression), we demonstrate that 1) 11% of individuals of an Icelandic population appear homoplasmic for ♂-type mitochondria in somatic tissues, 2) ♂-type mitochondrial genes are transcribed and 3) individuals with ♂-type mitochondria in somatic cells lose 30% of their wild-type respiratory capacity. This mitochondrial pattern in A. islandica is a special case of DUI, highlighted in individuals from both sexes with functional consequences at cellular and conceivably whole animal level.
Collapse
Affiliation(s)
- Cyril Dégletagne
- grid.10894.340000 0001 1033 7684Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany ,grid.7849.20000 0001 2150 7757Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, France
| | - Doris Abele
- grid.10894.340000 0001 1033 7684Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gernot Glöckner
- grid.6190.e0000 0000 8580 3777Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Benjamin Alric
- grid.7849.20000 0001 2150 7757Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, Villeurbanne, France
| | - Heike Gruber
- grid.419520.b0000 0001 2222 4708Max Planck Institute for Evolutionary Biology, Department of Evolutionary Theory, Plön, Germany
| | - Christoph Held
- grid.10894.340000 0001 1033 7684Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| |
Collapse
|
34
|
Chen W, Mao X. Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats. Ecol Evol 2021; 11:12003-12010. [PMID: 34522356 PMCID: PMC8427577 DOI: 10.1002/ece3.7966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial function needs strong interactions of mitochondrial and nuclear (mitonuclear) genomes, which can be disrupted by mitonuclear mismatch due to mitochondrial DNA (mtDNA) introgression between two formerly isolated populations or taxa. This mitonuclear disruption may cause severe cellular stress in mismatched individuals. Gene expression changes and alternative splicing (AS) are two important transcriptional regulations to respond to environmental or cellular stresses. We previously identified a naturally introgressed population in the intermediate horseshoe bat (Rhinolophus affinis). Individuals from this population belong to R. a. himalayanus and share almost identical nuclear genetic background; however, some of them had mtDNA from another subspecies (R. a. macrurus). With this unique natural system, we examined gene expression changes in six tissues between five mitonuclear mismatched and five matched individuals. A small number of differentially expressed genes (DEGs) were identified, and functional enrichment analysis revealed that most DEGs were related to immune response although some may be involved in response to oxidative stress. In contrast, we identified extensive AS events and alternatively spliced genes (ASGs) between mismatched and matched individuals. Functional enrichment analysis revealed that multiple ASGs were directly or indirectly associated with energy production in mitochondria which is vital for survival of organism. To our knowledge, this is the first study to examine the role of AS in responding to cellular stress caused by mitonuclear mismatch in natural populations. Our results suggest that AS may play a more important role than gene expression regulation in responding to severe environmental or cellular stresses.
Collapse
Affiliation(s)
- Wenli Chen
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Xiuguang Mao
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Institute of Eco‐Chongming (IEC)East China Normal UniversityShanghaiChina
| |
Collapse
|
35
|
Piccinini G, Iannello M, Puccio G, Plazzi F, Havird JC, Ghiselli F. Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves. Mol Biol Evol 2021; 38:2597-2614. [PMID: 33616640 PMCID: PMC8136519 DOI: 10.1093/molbev/msab054] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the “nuclear compensation hypothesis,” a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with “doubly uniparental” mtDNA inheritance. Our data showed strong and clear signals of mitonuclear coevolution. NuOXPHOS subunits had concordant topologies with mtOXPHOS subunits, contrary to previous phylogenies based on nuclear genes lacking mt interactions. Evolutionary rates between mt and nuOXPHOS subunits were also highly correlated compared with non-OXPHO-interacting nuclear genes. Nuclear subunits of chimeric OXPHOS complexes (I, III, IV, and V) also had higher dN/dS ratios than Complex II, which is formed exclusively by nuDNA-encoded subunits. However, we did not find evidence of nuclear compensation: mitochondria-encoded subunits showed similar dN/dS ratios compared with nuclear-encoded subunits, contrary to most previously studied bilaterian animals. Moreover, no site-specific signals of compensatory positive selection were detected in nuOXPHOS genes. Our analyses extend the evidence for mitonuclear coevolution to a new taxonomic group, but we propose a reconsideration of the nuclear compensation hypothesis.
Collapse
Affiliation(s)
- Giovanni Piccinini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| |
Collapse
|
36
|
Villacis-Perez E, Snoeck S, Kurlovs AH, Clark RM, Breeuwer JAJ, Van Leeuwen T. Adaptive divergence and post-zygotic barriers to gene flow between sympatric populations of a herbivorous mite. Commun Biol 2021; 4:853. [PMID: 34244609 PMCID: PMC8270941 DOI: 10.1038/s42003-021-02380-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Plant-herbivore interactions promote the generation and maintenance of both plant and herbivore biodiversity. The antagonistic interactions between plants and herbivores lead to host race formation: the evolution of herbivore types specializing on different plant species, with restricted gene flow between them. Understanding how ecological specialization promotes host race formation usually depends on artificial approaches, using laboratory experiments on populations associated with agricultural crops. However, evidence on how host races are formed and maintained in a natural setting remains scarce. Here, we take a multidisciplinary approach to understand whether populations of the generalist spider mite Tetranychus urticae form host races in nature. We demonstrate that a host race co-occurs among generalist conspecifics in the dune ecosystem of The Netherlands. Extensive field sampling and genotyping of individuals over three consecutive years showed a clear pattern of host associations. Genome-wide differences between the host race and generalist conspecifics were found using a dense set of SNPs on field-derived iso-female lines and previously sequenced genomes of T. urticae. Hybridization between lines of the host race and sympatric generalist lines is restricted by post-zygotic breakdown, and selection negatively impacts the survival of generalists on the native host of the host race. Our description of a host race among conspecifics with a larger diet breadth shows how ecological and reproductive isolation aid in maintaining intra-specific variation in sympatry, despite the opportunity for homogenization through gene flow. Our findings highlight the importance of explicitly considering the spatial and temporal scale on which plant-herbivore interactions occur in order to identify herbivore populations associated with different plant species in nature. This system can be used to study the underlying genetic architecture and mechanisms that facilitate the use of a large range of host plant taxa by extreme generalist herbivores. In addition, it offers the chance to investigate the prevalence and mechanisms of ecological specialization in nature.
Collapse
Affiliation(s)
- Ernesto Villacis-Perez
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Netherlands.
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
| | - Simon Snoeck
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- Department of Biology, University of Washington, Seattle, USA
| | - Andre H Kurlovs
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Richard M Clark
- School of Biological Sciences and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, USA
| | - Johannes A J Breeuwer
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, Netherlands.
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
| |
Collapse
|
37
|
Lukicheva S, Mardulyn P. Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles. Mol Ecol 2021; 30:4077-4089. [PMID: 34097806 DOI: 10.1111/mec.16011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023]
Abstract
A large number of genetic variation studies have identified cases of mitochondrial genome introgression in animals, indicating that reproductive barriers among closely related species are often permeable. Because of its sheer size, the impact of hybridization on the evolution of the nuclear genome is more difficult to apprehend. Only a few studies have explored it recently thanks to recent progress in DNA sequencing and genome assembly. Here, we analysed whole-genome sequence variation among multiple individuals of two sister species of leaf beetles inside their hybrid zone, in which asymmetric mitochondrial genome introgression had previously been established. We used a machine learning approach based on computer simulations for training to identify regions of the nuclear genome that were introgressed. We inferred asymmetric introgression of ≈2% of the genome, in the same direction that was observed for the mitochondrial genome. Because a previous study based on a reduced-representation sequencing approach was not able to detect this introgression, we conclude that whole-genome sequencing is necessary when the fraction of the introgressed genome is small. We also analysed the whole-genome sequence of a hybrid individual, demonstrating that hybrids have the capacity to backcross with the species for which virtually no introgression was observed. Our data suggest that one species has recently invaded the range of the other and/or some alleles that where transferred from the invaded into the invading species could be under positive selection and may have favoured the adaptation of the invading species to the Alpine environment.
Collapse
Affiliation(s)
- Svitlana Lukicheva
- Evolutionary Biology and Ecology, Interuniversity Institute of Bioinformatics in Brussels - (IB)², Université libre de Bruxelles, Brussels, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Interuniversity Institute of Bioinformatics in Brussels - (IB)², Université libre de Bruxelles, Brussels, Belgium
| |
Collapse
|
38
|
Coexistence of honeybees with distinct mitochondrial haplotypes and hybridised nuclear genomes on the Comoros Islands. Naturwissenschaften 2021; 108:17. [PMID: 33871694 DOI: 10.1007/s00114-021-01729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
The honeybee, Apis mellifera, is a globally distributed species that has spread both naturally and by humans across the globe resulting in many natural and secondary contact zones. The geographic isolation of honeybees is likely to contribute to genetic differentiation. Secondary contact has resulted in hybridization at the nuclear genome, but replacement of mitochondrial. Here, we used a mitochondrial marker and 19 microsatellite markers to test for the variations in the mitochondrial and nuclear genomes of honeybee populations on the Comoros islands. We used samples of 160 workers for mtDNA analysis and 288 workers from 16 colonies spread across the three islands for microsatellite analyses. Our results showed that the wild honeybee populations of the Comoros Islands consist of coexisting mitochondrial haplotypes. One belongs to the typical African A-lineage, and the other, the newly described L-lineage, is closely related to Apis koschevnikovi, a honeybee species native to Southeast Asia. The nuclear genomes show complete hybridization, high genetic diversity, and strong differentiation according to the island of origin. Based on our results, we hypothesise that the Asian honeybee could have been transported from Southeast Asia to Madagascar and Comoros via the human migrations that occurred 6000 years ago, and has hybridised with African honeybees at the nuclear genome, but maternal ancestry still can be traced using the mtDNA markers. We conclude that mtDNA plays a pivotal role in adaptation to the local environment, with both haplotypes of the honeybees of Comoros contributing significantly to the mito-nuclear coadaptation resulting in maintenance at almost equal frequency.
Collapse
|
39
|
Andersen MJ, McCullough JM, Gyllenhaal EF, Mapel XM, Haryoko T, Jønsson KA, Joseph L. Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds. Mol Ecol 2021; 30:2087-2103. [PMID: 33615597 PMCID: PMC8252742 DOI: 10.1111/mec.15856] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/02/2021] [Accepted: 02/12/2021] [Indexed: 01/03/2023]
Abstract
Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter, introgressed species may eventually have its own mtDNA replaced or “captured” by other species across its entire geographical range. Intermediate stages in the capture process should be observable. Two nonsister species of Australasian monarch‐flycatchers, Spectacled Monarch (Symposiachrus trivirgatus) mostly of Australia and Indonesia and Spot‐winged Monarch (S. guttula) of New Guinea, present an opportunity to observe this process. We analysed thousands of single nucleotide polymorphisms (SNPs) derived from ultraconserved elements of all subspecies of both species. Mitochondrial DNA sequences of Australian populations of S. trivirgatus form two paraphyletic clades, one being sister to and presumably introgressed by S. guttula despite little nuclear signal of introgression. Population genetic analyses (e.g., tests for modern and historical gene flow and selection) support at least one historical gene flow event between S. guttula and Australian S. trivirgatus. We also uncovered introgression from the Maluku Islands subspecies of S. trivirgatus into an island population of S. guttula, resulting in apparent nuclear paraphyly. We find that neutral demographic processes, not adaptive introgression, are the most likely cause of these complex population histories. We suggest that a Pleistocene extinction of S. guttula from mainland Australia resulted from range expansion by S. trivirgatus.
Collapse
Affiliation(s)
- Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Ethan F Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Xena M Mapel
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA.,Animal Genomics, ETH Zürich, Lindau, Switzerland
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Canberra, Australian Capital Territory, Australia
| |
Collapse
|
40
|
Zhou Y, Huang D, Xin Z, Xiao J. Evolution of Oxidative Phosphorylation (OXPHOS) Genes Reflecting the Evolutionary and Life Histories of Fig Wasps (Hymenoptera, Chalcidoidea). Genes (Basel) 2020; 11:genes11111353. [PMID: 33203150 PMCID: PMC7697784 DOI: 10.3390/genes11111353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/23/2022] Open
Abstract
Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps’ oxidative phosphorylation (OXPHOS) pathway, which is the main oxygen consumption and adenosine triphosphate (ATP) production system, may have adaptively evolved. In this study, we manually annotated the OXPHOS genes of 11 species of fig wasps, and compared the evolutionary patterns of OXPHOS genes for six pollinators and five non-pollinators. Thirteen mitochondrial protein-coding genes and 30 nuclear-coding single-copy orthologous genes were used to analyze the amino acid substitution rate and natural selection. The results showed high amino acid substitution rates of both mitochondrial and nuclear OXPHOS genes in fig wasps, implying the co-evolution of mitochondrial and nuclear genes. Our results further revealed that the OXPHOS-related genes evolved significantly faster in pollinators than in non-pollinators, and five genes had significant positive selection signals in the pollinator lineage, indicating that OXPHOS genes play an important role in the adaptation of pollinators. This study can help us understand the relationship between gene evolution and environmental adaptation.
Collapse
|
41
|
Kalyakulina A, Iannuzzi V, Sazzini M, Garagnani P, Jalan S, Franceschi C, Ivanchenko M, Giuliani C. Investigating Mitonuclear Genetic Interactions Through Machine Learning: A Case Study on Cold Adaptation Genes in Human Populations From Different European Climate Regions. Front Physiol 2020; 11:575968. [PMID: 33262703 PMCID: PMC7686538 DOI: 10.3389/fphys.2020.575968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/14/2020] [Indexed: 01/18/2023] Open
Abstract
Cold climates represent one of the major environmental challenges that anatomically modern humans faced during their dispersal out of Africa. The related adaptive traits have been achieved by modulation of thermogenesis and thermoregulation processes where nuclear (nuc) and mitochondrial (mt) genes play a major role. In human populations, mitonuclear genetic interactions are the result of both the peculiar genetic history of each human group and the different environments they have long occupied. This study aims to investigate mitonuclear genetic interactions by considering all the mitochondrial genes and 28 nuclear genes involved in brown adipose tissue metabolism, which have been previously hypothesized to be crucial for cold adaptation. For this purpose, we focused on three human populations (i.e., Finnish, British, and Central Italian people) of European ancestry from different biogeographical and climatic areas, and we used a machine learning approach to identify relevant nucDNA–mtDNA interactions that characterized each population. The obtained results are twofold: (i) at the methodological level, we demonstrated that a machine learning approach is able to detect patterns of genetic structure among human groups from different latitudes both at single genes and by considering combinations of mtDNA and nucDNA loci; (ii) at the biological level, the analysis identified population-specific nuclear genes and variants that likely play a relevant biological role in association with a mitochondrial gene (such as the “obesity gene” FTO in Finnish people). Further studies are needed to fully elucidate the evolutionary dynamics (e.g., migration, admixture, and/or local adaptation) that shaped these nucDNA–mtDNA interactions and their functional role.
Collapse
Affiliation(s)
- Alena Kalyakulina
- Department of Applied Mathematics, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Vincenzo Iannuzzi
- Alma Mater Research Institute on Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy.,Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Sarika Jalan
- Complex Systems Laboratory, Discipline of Physics, Indian Institute of Technology Indore, Indore, India.,Center for Theoretical Physics of Complex Systems, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Mikhail Ivanchenko
- Department of Applied Mathematics, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
42
|
Ågren JA, Munasinghe M, Clark AG. Mitochondrial-Y chromosome epistasis in Drosophila melanogaster. Proc Biol Sci 2020; 287:20200469. [PMID: 33081607 DOI: 10.1098/rspb.2020.0469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coordination between mitochondrial and nuclear genes is crucial to eukaryotic organisms. Predicting the nature of these epistatic interactions can be difficult because of the transmission asymmetry of the genes involved. While autosomes and X-linked genes are transmitted through both sexes, genes on the Y chromosome and in the mitochondrial genome are uniparentally transmitted through males and females, respectively. Here, we generate 36 otherwise isogenic Drosophila melanogaster strains differing only in the geographical origin of their mitochondrial genome and Y chromosome, to experimentally examine the effects of the uniparentally inherited parts of the genome, as well as their interaction, in males. We assay longevity and gene expression through RNA-sequencing. We detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis. In particular, genes involved in male reproduction appear to be especially sensitive to such interactions, and variation on the Y chromosome is associated with differences in longevity. Despite these interactions, we find no evidence that the mitochondrial genome and Y chromosome are co-adapted within a geographical region. Overall, our study demonstrates a key role for the uniparentally inherited parts of the genome for male biology, but also that mito-nuclear interactions are complex and not easily predicted from simple transmission asymmetries.
Collapse
Affiliation(s)
- J Arvid Ågren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Manisha Munasinghe
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.,Department of Computational Biology, Cornell University, Ithaca, NY, USA
| |
Collapse
|
43
|
Abstract
New species arise as the genomes of populations diverge. The developmental 'alarm clock' of speciation sounds off when sufficient divergence in genetic control of development leads hybrid individuals to infertility or inviability, the world awoken to the dawn of new species with intrinsic post-zygotic reproductive isolation. Some developmental stages will be more prone to hybrid dysfunction due to how molecular evolution interacts with the ontogenetic timing of gene expression. Considering the ontogeny of hybrid incompatibilities provides a profitable connection between 'evo-devo' and speciation genetics to better link macroevolutionary pattern, microevolutionary process, and molecular mechanisms. Here, we explore speciation alongside development, emphasizing their mutual dependence on genetic network features, fitness landscapes, and developmental system drift. We assess models for how ontogenetic timing of reproductive isolation can be predictable. Experiments and theory within this synthetic perspective can help identify new rules of speciation as well as rules in the molecular evolution of development.
Collapse
Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| | - Joanna D Bundus
- Department of Integrative Biology, University of Wisconsin – MadisonMadisonUnited States
| |
Collapse
|
44
|
An J, Zheng W, Liang J, Xi Q, Chen R, Jia J, Lu X, Jakovlić I. Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness. BMC Genomics 2020; 21:607. [PMID: 32883208 PMCID: PMC7469299 DOI: 10.1186/s12864-020-07021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea. RESULTS It exhibited a barcode (cox1) similarity level of only 87-89% with North-American populations, which is unusually low for conspecifics. Its mitogenome is among the largest in isopods (≈16.5 Kbp), mostly due to a large duplicated palindromic genomic segment (2 Kbp) comprising three genes. However, it lost a segment comprising three genes, nad4L-trnP-nad6, and many genes exhibited highly divergent sequences in comparison to isopod orthologues, including numerous mutations, deletions and insertions. Phylogenetic and selection analyses corroborated that this is one of the handful of most rapidly evolving available isopod mitogenomes, and that it evolves under highly relaxed selection constraints (as opposed to positive selection). However, its nuclear 18S gene is highly conserved, which suggests that rapid evolution is limited to its mitochondrial genome. The cox1 sequence analysis indicates that elevated mitogenomic evolutionary rates are not shared by North-American conspecifics, which suggests a breakdown of cox1 barcoding in this species. CONCLUSIONS A highly architecturally disrupted mitogenome and decoupling of mitochondrial and nuclear rates would normally be expected to have strong negative impacts on the fitness of the organism, so the existence of this lineage is a puzzling evolutionary question. Additional studies are needed to assess the phylogenetic breadth of this disrupted mitochondrial architecture and its impact on fitness.
Collapse
Affiliation(s)
- Jianmei An
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China.
| | - Wanrui Zheng
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Jielong Liang
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Qianqian Xi
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ruru Chen
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Junli Jia
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Xia Lu
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, 430075, Hubei, PR China
| |
Collapse
|
45
|
Getmantseva L, Bakoev S, Bakoev N, Karpushkina T, Kostyunina O. Mitochondrial DNA Diversity in Large White Pigs in Russia. Animals (Basel) 2020; 10:E1365. [PMID: 32781729 PMCID: PMC7460241 DOI: 10.3390/ani10081365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022] Open
Abstract
The Large White pig is the most commonly raised commercial pig breed in the world. The aim of this work was to investigate D-loop mtDNA in Large White pigs (n = 402) of various selections bred in the Russian Federation from 2000 to 2019. The general sample consisted of three groups: Old (n = 78) (Russian selection, 2000-2010); Imp (n = 123) (imported to Russia in 2008-2014); New (n = 201) (2015-2019). The synthesized score (Fz) was calculated by analyzing the main PCA (principal component analysis components). An affiliation to Asian or European haplogroups was determined according to the NCBI (National Center for Biotechnology Information). In the study, we defined 46 polymorphic sites and 42 haplotypes. Significant distinctions between groups Old, Imp and New in frequencies of haplotypes and haplogroups were established. The distribution of Asian and European haplotypes in the groups was Old: 50%/50%, Imp: 43%/57%, New: 75%/25%, respectively. The variety of haplotypes and haplogroups in the pigs of the group New is related to the farms in which they breed. Haplotype frequencies significantly differ between the clusters Old_Center, Old_Siberia and Old_South. This study will provide information on the genetic diversity of Large White breed pigs. The results will be useful for the conservation and sustainable use of these resources.
Collapse
Affiliation(s)
- Lyubov Getmantseva
- Federal Science Center for Animal Husbandry Named after Academy Member L.K. Ernst, Dubrovitsy 142132, Russia; (S.B.); (N.B.); (T.K.); (O.K.)
| | | | | | | | | |
Collapse
|
46
|
Wilson RE, Sonsthagen SA, Smé N, Gharrett AJ, Majewski AR, Wedemeyer K, Nelson RJ, Talbot SL. Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biol 2020. [DOI: 10.1007/s00300-020-02703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
47
|
Ruiz MB, Taverna A, Servetto N, Sahade R, Held C. Hidden diversity in Antarctica: Molecular and morphological evidence of two different species within one of the most conspicuous ascidian species. Ecol Evol 2020; 10:8127-8143. [PMID: 32788966 PMCID: PMC7417227 DOI: 10.1002/ece3.6504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
The Southern Ocean is one of the most isolated marine ecosystems, characterized by high levels of endemism, diversity, and biomass. Ascidians are among the dominant groups in Antarctic benthic assemblages; thus, recording the evolutionary patterns of this group is crucial to improve our current understanding of the assembly of this polar ocean. We studied the genetic variation within Cnemidocarpa verrucosa sensu lato, one of the most widely distributed abundant and studied ascidian species in Antarctica. Using a mitochondrial and a nuclear gene (COI and 18S), the phylogeography of fifteen populations distributed along the West Antarctic Peninsula and Burdwood Bank/MPA Namuncurá (South American shelf) was characterized, where the distribution of the genetic distance suggested the existence of, at least, two species within nominal C. verrucosa. When reevaluating morphological traits to distinguish between genetically defined species, the presence of a basal disk in one of the genotypes could be a diagnostic morphological trait to differentiate the species. These results are surprising due to the large research that has been carried out with the conspicuous C. verrucosa with no differentiation between species. Furthermore, it provides important tools to distinguish species in the field and laboratory. But also, these results give new insights into patterns of differentiation between closely related species that are distributed in sympatry, where the permeability of species boundaries still needs to be well understood.
Collapse
Affiliation(s)
- Micaela B. Ruiz
- Instituto de Diversidad y Ecología Animal (IDEA)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CórdobaArgentina
- Facultad de Ciencias Exactas Físicas y NaturalesDepartamento de Diversidad Biológica y Ecología, Ecología MarinaUniversidad Nacional de CórdobaCórdobaArgentina
| | - Anabela Taverna
- Instituto de Diversidad y Ecología Animal (IDEA)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CórdobaArgentina
- Facultad de Ciencias Exactas Físicas y NaturalesDepartamento de Diversidad Biológica y Ecología, Ecología MarinaUniversidad Nacional de CórdobaCórdobaArgentina
| | - Natalia Servetto
- Instituto de Diversidad y Ecología Animal (IDEA)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CórdobaArgentina
- Facultad de Ciencias Exactas Físicas y NaturalesDepartamento de Diversidad Biológica y Ecología, Ecología MarinaUniversidad Nacional de CórdobaCórdobaArgentina
| | - Ricardo Sahade
- Instituto de Diversidad y Ecología Animal (IDEA)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)CórdobaArgentina
- Facultad de Ciencias Exactas Físicas y NaturalesDepartamento de Diversidad Biológica y Ecología, Ecología MarinaUniversidad Nacional de CórdobaCórdobaArgentina
| | - Christoph Held
- Section Functional Ecology, Evolutionary MacroecologyAlfred Wegener Institute Helmholtz‐Zentrum für Polar‐ und MeeresforschungBremerhavenGermany
| |
Collapse
|
48
|
An Unusual Amino Acid Substitution Within Hummingbird Cytochrome c Oxidase Alters a Key Proton-Conducting Channel. G3-GENES GENOMES GENETICS 2020; 10:2477-2485. [PMID: 32444359 PMCID: PMC7341133 DOI: 10.1534/g3.120.401312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hummingbirds in flight exhibit the highest mass-specific metabolic rate of all vertebrates. The bioenergetic requirements associated with sustained hovering flight raise the possibility of unique amino acid substitutions that would enhance aerobic metabolism. Here, we have identified a non-conservative substitution within the mitochondria-encoded cytochrome c oxidase subunit I (COI) that is fixed within hummingbirds, but not among other vertebrates. This unusual change is also rare among metazoans, but can be identified in several clades with diverse life histories. We performed atomistic molecular dynamics simulations using bovine and hummingbird COI models, thereby bypassing experimental limitations imposed by the inability to modify mtDNA in a site-specific manner. Intriguingly, our findings suggest that COI amino acid position 153 (bovine numbering convention) provides control over the hydration and activity of a key proton channel in COX. We discuss potential phenotypic outcomes linked to this alteration encoded by hummingbird mitochondrial genomes.
Collapse
|
49
|
Rank NE, Mardulyn P, Heidl SJ, Roberts KT, Zavala NA, Smiley JT, Dahlhoff EP. Mitonuclear mismatch alters performance and reproductive success in naturally introgressed populations of a montane leaf beetle. Evolution 2020; 74:1724-1740. [PMID: 32246837 DOI: 10.1111/evo.13962] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/22/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle Chrysomela aeneicollis was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial cytochrome oxidase II (COII) and the nuclear gene phosphoglucose isomerase (PGI) shows concordance and was significantly greater along a 65 km transect than 10 other loci. STRUCTURE analyses using neutral loci identified a southern and northern subpopulation, which interbreed in the central drainage Bishop Creek. COII and PGI were used as indicators of mitochondrial and nuclear genetic variation in field and laboratory experiments conducted on beetles from this admixed population. Fecundity, larval development rate, running speed and male mating frequency were higher for beetles with geographically "matched" than "mismatched" mitonuclear genotypes. Effects of mitonuclear mismatch were largest for individuals with northern nuclear genotypes possessing southern mitochondria and were most pronounced after heat treatment or at high elevation. These findings suggest that mitonuclear incompatibility diminishes performance and reproductive success in nature, effects that could intensify at environmental extremes.
Collapse
Affiliation(s)
- Nathan E Rank
- Department of Biology, Sonoma State University, Rohnert Park, California, 94928.,White Mountain Research Center, University of California, Bishop, California, 93514
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, 1050, Belgium
| | - Sarah J Heidl
- Department of Biology, Sonoma State University, Rohnert Park, California, 94928.,White Mountain Research Center, University of California, Bishop, California, 93514
| | - Kevin T Roberts
- Department of Biology, Sonoma State University, Rohnert Park, California, 94928.,White Mountain Research Center, University of California, Bishop, California, 93514.,Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Nicolas A Zavala
- White Mountain Research Center, University of California, Bishop, California, 93514.,Department of Biology, Santa Clara University, Santa Clara, California, 95053
| | - John T Smiley
- White Mountain Research Center, University of California, Bishop, California, 93514
| | - Elizabeth P Dahlhoff
- White Mountain Research Center, University of California, Bishop, California, 93514.,Department of Biology, Santa Clara University, Santa Clara, California, 95053
| |
Collapse
|
50
|
Strong selective effects of mitochondrial DNA on the nuclear genome. Proc Natl Acad Sci U S A 2020; 117:6616-6621. [PMID: 32156736 DOI: 10.1073/pnas.1910141117] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod Tigriopus californicus to disrupt putatively coevolved mitonuclear genotypes in reciprocal F2 hybrids. We utilized interindividual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and in vitro ATP synthesis rates of mitochondria isolated from high-fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low-fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high- or low-fitness hybrids. Significant biases for maternal alleles were detected on 5 (of 12) chromosomes in high-fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low-fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that intergenomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.
Collapse
|