1
|
Vassall M, Chakraborty S, Feng Y, Faheem M, Wang X, Bhandari RK. Transcriptional Alterations Induced by Delta-9 Tetrahydrocannabinol in the Brain and Gonads of Adult Medaka. J Xenobiot 2023; 13:237-251. [PMID: 37367494 DOI: 10.3390/jox13020018] [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: 04/18/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 06/28/2023] Open
Abstract
With the legalization of marijuana smoking in several states of the United States and many other countries for medicinal and recreational use, the possibility of its release into the environment cannot be overruled. Currently, the environmental levels of marijuana metabolites are not monitored on a regular basis, and their stability in the environment is not well understood. Laboratory studies have linked delta 9-tetrahydrocannabinol (Δ9-THC) exposure with behavioral abnormalities in some fish species; however, their effects on endocrine organs are less understood. To understand the effects of THC on the brain and gonads, we exposed adult medaka (Oryzias latipes, Hd-rR strain, both male and female) to 50 ug/L THC for 21 days spanning their complete spermatogenic and oogenic cycles. We examined transcriptional responses of the brain and gonads (testis and ovary) to Δ9-THC, particularly molecular pathways associated with behavioral and reproductive functions. The Δ9-THC effects were more profound in males than females. The Δ9-THC-induced differential expression pattern of genes in the brain of the male fish suggested pathways to neurodegenerative diseases and pathways to reproductive impairment in the testis. The present results provide insights into endocrine disruption in aquatic organisms due to environmental cannabinoid compounds.
Collapse
Affiliation(s)
- Marlee Vassall
- Department of Biology, University of North Carolina, Greensboro, NC 27412, USA
| | - Sourav Chakraborty
- Department of Biology, University of North Carolina, Greensboro, NC 27412, USA
| | - Yashi Feng
- Department of Biology, University of North Carolina, Greensboro, NC 27412, USA
| | - Mehwish Faheem
- Department of Biology, University of North Carolina, Greensboro, NC 27412, USA
| | - Xuegeng Wang
- Department of Biology, University of North Carolina, Greensboro, NC 27412, USA
- Institute of Modern Aquaculture Science and Engineering, College of Life Sciences, South China Normal University, Guangzhou 510631, China
| | | |
Collapse
|
2
|
Watson ET, Flanagan BA, Pascar JA, Edmands S. Mitochondrial effects on fertility and longevity in Tigriopus californicus contradict predictions of the mother's curse hypothesis. Proc Biol Sci 2022; 289:20221211. [PMID: 36382523 PMCID: PMC9667352 DOI: 10.1098/rspb.2022.1211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
Strict maternal inheritance of mitochondria favours the evolutionary accumulation of sex-biased fitness effects, as mitochondrial evolution occurs exclusively in female lineages. The 'mother's curse' hypothesis proposes that male-harming mutations should accumulate in mitochondrial genomes when they have neutral or beneficial effects on female fitness. Rigorous empirical tests have largely focused on Drosophila, where support for the predictions of mother's curse has been mixed. We investigated the impact of mother's curse mutations in Tigriopus californicus, a minute crustacean. Using non-recombinant backcrosses, we introgressed four divergent mitochondrial haplotypes into two nuclear backgrounds and recorded measures of fertility and longevity. We found that the phenotypic effects of mitochondrial mutations were context dependent, being influenced by the nuclear background in which they were expressed, as well as the sex of the individual and rearing temperature. Mitochondrial haplotype effects were greater for fertility than longevity, and temperature effects were greater for longevity. However, in opposition to mother's curse expectations, females had higher mitochondrial genetic variance than males for fertility and longevity, little evidence of sexual antagonism favouring females was found, and the impacts of mitonuclear mismatch harmed females but not males. Together, this indicates that selection on mitochondrial variation has not resulted in the accumulation of male mutation load in Tigriopus californicus.
Collapse
Affiliation(s)
- Eric T. Watson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0001, USA
| | - Ben A. Flanagan
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0001, USA
| | - Jane A. Pascar
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0001, USA
| | - Suzanne Edmands
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0001, USA
| |
Collapse
|
3
|
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
|
4
|
Powers MJ, Martz LD, Burton RS, Hill GE, Weaver RJ. Evidence for hybrid breakdown in production of red carotenoids in the marine invertebrate Tigriopus californicus. PLoS One 2021; 16:e0259371. [PMID: 34748608 PMCID: PMC8575244 DOI: 10.1371/journal.pone.0259371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/18/2021] [Indexed: 11/21/2022] Open
Abstract
The marine copepod, Tigriopus californicus, produces the red carotenoid pigment astaxanthin from yellow dietary precursors. This ‘bioconversion’ of yellow carotenoids to red is hypothesized to be linked to individual condition, possibly through shared metabolic pathways with mitochondrial oxidative phosphorylation. Experimental inter-population crosses of lab-reared T. californicus typically produces low-fitness hybrids is due in large part to the disruption of coadapted sets nuclear and mitochondrial genes within the parental populations. These hybrid incompatibilities can increase variability in life history traits and energy production among hybrid lines. Here, we tested if production of astaxanthin was compromised in hybrid copepods and if it was linked to mitochondrial metabolism and offspring development. We observed no clear mitonuclear dysfunction in hybrids fed a limited, carotenoid-deficient diet of nutritional yeast. However, when yellow carotenoids were restored to their diet, hybrid lines produced less astaxanthin than parental lines. We observed that lines fed a yeast diet produced less ATP and had slower offspring development compared to lines fed a more complete diet of algae, suggesting the yeast-only diet may have obscured effects of mitonuclear dysfunction. Astaxanthin production was not significantly associated with development among lines fed a yeast diet but was negatively related to development in early generation hybrids fed an algal diet. In lines fed yeast, astaxanthin was negatively related to ATP synthesis, but in lines fed algae, the relationship was reversed. Although the effects of the yeast diet may have obscured evidence of hybrid dysfunction, these results suggest that astaxanthin bioconversion may still be related to mitochondrial performance and reproductive success.
Collapse
Affiliation(s)
- Matthew J. Powers
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
- * E-mail: (MJP); (LDM)
| | - Lucas D. Martz
- University of California, Scripps Institution of Oceanography, San Diego, CA, United States of America
- * E-mail: (MJP); (LDM)
| | - Ronald S. Burton
- University of California, Scripps Institution of Oceanography, San Diego, CA, United States of America
| | - Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Ryan J. Weaver
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, United States of America
| |
Collapse
|
5
|
Brown JA, Sammy MJ, Ballinger SW. An evolutionary, or "Mitocentric" perspective on cellular function and disease. Redox Biol 2020; 36:101568. [PMID: 32512469 PMCID: PMC7281786 DOI: 10.1016/j.redox.2020.101568] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/01/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
The incidence of common, metabolic diseases (e.g. obesity, cardiovascular disease, diabetes) with complex genetic etiology has been steadily increasing nationally and globally. While identification of a genetic model that explains susceptibility and risk for these diseases has been pursued over several decades, no clear paradigm has yet been found to disentangle the genetic basis of polygenic/complex disease development. Since the evolution of the eukaryotic cell involved a symbiotic interaction between the antecedents of the mitochondrion and nucleus (which itself is a genetic hybrid), we suggest that this history provides a rational basis for investigating whether genetic interaction and co-evolution of these genomes still exists. We propose that both mitochondrial and Mendelian, or "mito-Mendelian" genetics play a significant role in cell function, and thus disease risk. This paradigm contemplates the natural variation and co-evolution of both mitochondrial and nuclear DNA backgrounds on multiple mitochondrial functions that are discussed herein, including energy production, cell signaling and immune response, which collectively can influence disease development. At the nexus of these processes is the economy of mitochondrial metabolism, programmed by both mitochondrial and nuclear genomes.
Collapse
Affiliation(s)
- Jamelle A Brown
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Melissa J Sammy
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Scott W Ballinger
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| |
Collapse
|
6
|
Yan Z, Ye G, Werren JH. Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects. Mol Biol Evol 2019; 36:1022-1036. [PMID: 30785203 DOI: 10.1093/molbev/msz036] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex.
Collapse
Affiliation(s)
- Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Department of Biology, University of Rochester, Rochester, NY
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY
| |
Collapse
|
7
|
Barbhuiya PA, Uddin A, Chakraborty S. Genome‐wide comparison of codon usage dynamics in mitochondrial genes across different species of amphibian genus
Bombina. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:99-112. [DOI: 10.1002/jez.b.22852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/10/2019] [Accepted: 03/20/2019] [Indexed: 01/16/2023]
Affiliation(s)
| | - Arif Uddin
- Department of ZoologyMoinul Hoque Choudhury Memorial Science CollegeHailakandi Assam India
| | | |
Collapse
|
8
|
Harada AE, Healy TM, Burton RS. Variation in Thermal Tolerance and Its Relationship to Mitochondrial Function Across Populations of Tigriopus californicus. Front Physiol 2019; 10:213. [PMID: 30930787 PMCID: PMC6429002 DOI: 10.3389/fphys.2019.00213] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Variation in thermal tolerance plays a key role in determining the biogeographic distribution of organisms. Consequently, identifying the mechanistic basis for thermal tolerance is necessary for understanding not only current species range limits but also the capacity for range limits to shift in response to climate change. Although variation in mitochondrial function likely contributes to variation in thermal tolerance, the extent to which mitochondrial function underlies local thermal adaptation is not fully understood. In the current study, we examine variation in thermal tolerance and mitochondrial function among three populations of the intertidal copepod Tigriopus californicus found across a latitudinal thermal gradient along the coast of California, USA. We tested (1) acute thermal tolerance using survivorship and knockdown assays, (2) chronic thermal tolerance using survivorship of nauplii and developmental rate, and (3) mitochondrial performance at a range of temperatures using ATP synthesis fueled by complexes I, II, and I&II, as well as respiration of permeabilized fibers. We find evidence for latitudinal thermal adaptation: the southernmost San Diego population outperforms the northernmost Santa Cruz in measures of survivorship, knockdown temperature, and ATP synthesis rates during acute thermal exposures. However, under a chronic thermal regime, survivorship and developmental rate are more similar in the southernmost and northernmost population than in the mid-range population (Abalone Cove). Though this pattern is unexpected, it aligns well with population-specific rates of ATP synthesis at these chronic temperatures. Combined with the tight correlation of ATP synthesis decline and knockdown temperature, these data suggest a role for mitochondria in setting thermal range limits and indicate that divergence in mitochondrial function is likely a component of adaptation across latitudinal thermal gradients.
Collapse
Affiliation(s)
- Alice E Harada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - 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
|
9
|
Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC. Cytonuclear integration and co-evolution. Nat Rev Genet 2018; 19:635-648. [PMID: 30018367 PMCID: PMC6469396 DOI: 10.1038/s41576-018-0035-9] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The partitioning of genetic material between the nucleus and cytoplasmic (mitochondrial and plastid) genomes within eukaryotic cells necessitates coordinated integration between these genomic compartments, with important evolutionary and biomedical implications. Classic questions persist about the pervasive reduction of cytoplasmic genomes via a combination of gene loss, transfer and functional replacement - and yet why they are almost always retained in some minimal form. One striking consequence of cytonuclear integration is the existence of 'chimeric' enzyme complexes composed of subunits encoded in two different genomes. Advances in structural biology and comparative genomics are yielding important insights into the evolution of such complexes, including correlated sequence changes and recruitment of novel subunits. Thus, chimeric cytonuclear complexes provide a powerful window into the mechanisms of molecular co-evolution.
Collapse
Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
10
|
Haenel GJ, Del Gaizo Moore V. Functional Divergence of Mitochondria and Coevolution of Genomes: Cool Mitochondria in Hot Lizards. Physiol Biochem Zool 2018; 91:1068-1081. [DOI: 10.1086/699918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
11
|
Havird JC, Trapp P, Miller CM, Bazos I, Sloan DB. Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage. Genome Biol Evol 2018; 9:323-336. [PMID: 28164243 PMCID: PMC5381668 DOI: 10.1093/gbe/evx010] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 12/23/2022] Open
Abstract
Understanding mechanisms of coevolution between nuclear and mitochondrial (mt) genomes is a defining challenge in eukaryotic genetics. The angiosperm genus Silene is a natural system to investigate the causes and consequences of mt mutation rate variation because closely related species have highly divergent rates. In Silene species with fast-evolving mtDNA, nuclear genes that encode mitochondrially targeted proteins (N-mt genes) are also fast-evolving. This correlation could indicate positive selection to compensate for mt mutations, but might also result from a recent relaxation of selection. To differentiate between these interpretations, we used phylogenetic and population-genetic methods to test for positive and relaxed selection in three classes of N-mt genes (oxidative phosphorylation genes, ribosomal genes, and “RRR” genes involved in mtDNA recombination, replication, and repair). In all three classes, we found that species with fast-evolving mtDNA had: 1) elevated dN/dS, 2) an excess of nonsynonymous divergence relative to levels of intraspecific polymorphism, which is a signature of positive selection, and 3) no clear signals of relaxed selection. “Control” genes exhibited comparatively few signs of positive selection. These results suggest that high mt mutation rates can create selection on N-mt genes and that relaxed selection is an unlikely cause of recent accelerations in the evolution of N-mt genes. Because mt-RRR genes were found to be under positive selection, it is unlikely that elevated mt mutation rates in Silene were caused by inactivation of these mt-RRR genes. Therefore, the causes of extreme increases in angiosperm mt mutation rates remain uncertain.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Paul Trapp
- Department of Biology, Colorado State University, Fort Collins, CO
| | | | - Ioannis Bazos
- Department of Ecology and Systematics, National and Kapodistrian University of Athens, Panepistimiopolis, Greece
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| |
Collapse
|
12
|
Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
| |
Collapse
|
13
|
Sloan DB, Havird JC, Sharbrough J. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Mol Ecol 2017; 26:2212-2236. [PMID: 27997046 PMCID: PMC6534505 DOI: 10.1111/mec.13959] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
The study of reproductive isolation and species barriers frequently focuses on mitochondrial genomes and has produced two alternative and almost diametrically opposed narratives. On one hand, mtDNA may be at the forefront of speciation events, with co-evolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted. We argue that these seemingly contradictory patterns can result from a single underlying cause. Specifically, the accumulation of deleterious mutations in mtDNA creates a problem with two alternative evolutionary solutions. In some cases, compensatory or epistatic changes in the nuclear genome may ameliorate the effects of mitochondrial mutations, thereby establishing coadapted mitonuclear genotypes within populations and forming the basis of reproductive incompatibilities between populations. Alternatively, populations with high mitochondrial mutation loads may be rescued by replacement with a more fit, foreign mitochondrial haplotype. Coupled with many nonadaptive mechanisms of introgression that can preferentially affect cytoplasmic genomes, this form of adaptive introgression may contribute to the widespread discordance between mitochondrial and nuclear genealogies. Here, we review recent advances related to mitochondrial introgression and mitonuclear incompatibilities, including the potential for cointrogression of mtDNA and interacting nuclear genes. We also address an emerging controversy over the classic assumption that selection on mitochondrial genomes is inefficient and discuss the mechanisms that lead lineages down alternative evolutionary paths in response to mitochondrial mutation accumulation.
Collapse
Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| |
Collapse
|
14
|
Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C. Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Front Genet 2017; 8:25. [PMID: 28316610 PMCID: PMC5334354 DOI: 10.3389/fgene.2017.00025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
Collapse
Affiliation(s)
- Paul Sunnucks
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Hernán E. Morales
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
- Department of Marine Sciences, University of GothenburgGothenburg, Sweden
| | - Annika M. Lamb
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| |
Collapse
|
15
|
Porplycia D, Lau GY, McDonald J, Chen Z, Richards JG, Moyes CD. Subfunctionalization of COX4 paralogs in fish. Am J Physiol Regul Integr Comp Physiol 2017; 312:R671-R680. [PMID: 28148493 DOI: 10.1152/ajpregu.00479.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/23/2017] [Accepted: 01/31/2017] [Indexed: 12/15/2022]
Abstract
Cytochrome c oxidase (COX) subunit 4 has two paralogs in most vertebrates. The mammalian COX4-2 gene is hypoxia responsive, and the protein has a disrupted ATP-binding site that confers kinetic properties on COX that distinguish it from COX4-1. The structure-function of COX4-2 orthologs in other vertebrates remains uncertain. Phylogenetic analyses suggest the two paralogs arose in basal vertebrates, but COX4-2 orthologs diverged faster than COX4-1 orthologs. COX4-1/4-2 protein levels in tilapia tracked mRNA levels across tissues, and did not change in hypoxia, arguing against a role for differential post-translational regulation of paralogs. The heart, and to a lesser extent the brain, showed a size-dependent shift from COX4-1 to COX4-2 (transcript and protein). ATP allosterically inhibited both velocity and affinity for oxygen in COX assayed from both muscle (predominantly COX4-2) and gill (predominantly COX4-1). We saw some evidence of cellular and subcellular discrimination of COX4 paralogs in heart. In cardiac ventricle, some non-cardiomyocyte cells were COX positive but lacked detectible COX4-2. Within heart, the two proteins partitioned to different mitochondrial subpopulations. Cardiac subsarcolemmal mitochondria had mostly COX4-1 and intermyofibrillar mitochondria had mostly COX4-2. Collectively, these data argue that, despite common evolutionary origins, COX4-2 orthologs of fish show unique patterns of subfunctionalization with respect to transcriptional and posttranslation regulation relative to the rodents and primates that have been studied to date.
Collapse
Affiliation(s)
- Danielle Porplycia
- Department of Biology, Queen's University, Kingston, Ontario, Canada; and
| | - Gigi Y Lau
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jared McDonald
- Department of Biology, Queen's University, Kingston, Ontario, Canada; and
| | - Zhilin Chen
- Department of Biology, Queen's University, Kingston, Ontario, Canada; and
| | - Jeffrey G Richards
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | | |
Collapse
|
16
|
Đorđević M, Stojković B, Savković U, Immonen E, Tucić N, Lazarević J, Arnqvist G. Sex-specific mitonuclear epistasis and the evolution of mitochondrial bioenergetics, ageing, and life history in seed beetles. Evolution 2016; 71:274-288. [PMID: 27861795 DOI: 10.1111/evo.13109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/13/2016] [Accepted: 10/24/2016] [Indexed: 12/23/2022]
Abstract
The role of mitochondrial DNA for the evolution of life-history traits remains debated. We examined mitonuclear effects on the activity of the multisubunit complex of the electron transport chain (ETC) involved in oxidative phosphorylation (OXPHOS) across lines of the seed beetle Acanthoscelides obtectus selected for a short (E) or a long (L) life for more than >160 generations. We constructed and phenotyped mitonuclear introgression lines, which allowed us to assess the independent effects of the evolutionary history of the nuclear and the mitochondrial genome. The nuclear genome was responsible for the largest share of divergence seen in ageing. However, the mitochondrial genome also had sizeable effects, which were sex-specific and expressed primarily as epistatic interactions with the nuclear genome. The effects of mitonuclear disruption were largely consistent with mitonuclear coadaptation. Variation in ETC activity explained a large proportion of variance in ageing and life-history traits and this multivariate relationship differed somewhat between the sexes. In conclusion, mitonuclear epistasis has played an important role in the laboratory evolution of ETC complex activity, ageing, and life histories and these are closely associated. The mitonuclear architecture of evolved differences in life-history traits and mitochondrial bioenergetics was sex-specific.
Collapse
Affiliation(s)
- Mirko Đorđević
- Department of Evolutionary Biology, Institute for Biological Research, University of Belgrade, Despota Stefana Boulevard 142, Belgrade, 11060, Serbia
| | - Biljana Stojković
- Department of Evolutionary Biology, Institute for Biological Research, University of Belgrade, Despota Stefana Boulevard 142, Belgrade, 11060, Serbia.,Institute of Zoology, Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Uroš Savković
- Department of Evolutionary Biology, Institute for Biological Research, University of Belgrade, Despota Stefana Boulevard 142, Belgrade, 11060, Serbia
| | - Elina Immonen
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Nikola Tucić
- Department of Evolutionary Biology, Institute for Biological Research, University of Belgrade, Despota Stefana Boulevard 142, Belgrade, 11060, Serbia
| | - Jelica Lazarević
- Department of Insect Physiology and Biochemistry, Institute for Biological Research, University of Belgrade, Despota Stefana Boulevard 142, Belgrade, 11060, Serbia
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| |
Collapse
|
17
|
Intraspecific genetic variation in hosts affects regulation of obligate heritable symbionts. Proc Natl Acad Sci U S A 2016; 113:13114-13119. [PMID: 27799532 DOI: 10.1073/pnas.1610749113] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Symbiotic relationships promote biological diversification by unlocking new ecological niches. Over evolutionary time, hosts and symbionts often enter intimate and permanent relationships, which must be maintained and regulated for both lineages to persist. Many insect species harbor obligate, heritable symbiotic bacteria that provision essential nutrients and enable hosts to exploit niches that would otherwise be unavailable. Hosts must regulate symbiont population sizes, but optimal regulation may be affected by the need to respond to the ongoing evolution of symbionts, which experience high levels of genetic drift and potential selection for selfish traits. We address the extent of intraspecific variation in the regulation of a mutually obligate symbiosis, between the pea aphid (Acyrthosiphon pisum) and its maternally transmitted symbiont, Buchnera aphidicola Using experimental crosses to identify effects of host genotypes, we measured symbiont titer, as the ratio of genomic copy numbers of symbiont and host, as well as developmental time and fecundity of hosts. We find a large (>10-fold) range in symbiont titer among genetically distinct aphid lines harboring the same Buchnera haplotype. Aphid clones also vary in fitness, measured as developmental time and fecundity, and genetically based variation in titer is correlated with host fitness, with higher titers corresponding to lower reproductive rates of hosts. Our work shows that obligate symbiosis is not static but instead is subject to short-term evolutionary dynamics, potentially reflecting coevolutionary interactions between host and symbiont.
Collapse
|
18
|
Sloan DB, Fields PD, Havird JC. Mitonuclear linkage disequilibrium in human populations. Proc Biol Sci 2016; 282:rspb.2015.1704. [PMID: 26378221 DOI: 10.1098/rspb.2015.1704] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.
Collapse
Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Peter D Fields
- Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
19
|
Easton EE, Thistle D. Do some deep‐sea, sediment‐dwelling species of harpacticoid copepods have 1000‐km‐scale range sizes? Mol Ecol 2016; 25:4301-18. [DOI: 10.1111/mec.13744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- E. E. Easton
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| | - D. Thistle
- Department of Earth, Ocean and Atmospheric Science Florida State University Tallahassee FL 32306‐4320 USA
| |
Collapse
|
20
|
Pereira RJ, Barreto FS, Pierce NT, Carneiro M, Burton RS. Transcriptome-wide patterns of divergence during allopatric evolution. Mol Ecol 2016; 25:1478-93. [DOI: 10.1111/mec.13579] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/03/2015] [Accepted: 01/06/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Ricardo J. Pereira
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Felipe S. Barreto
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
- Department of Integrative Biology; Oregon State University; Corvallis OR 97331 USA
| | - N. Tessa Pierce
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
| | - Miguel Carneiro
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão 4485-661 Vairão Portugal
| | - Ronald S. Burton
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California, San Diego; La Jolla CA 92093-0202 USA
| |
Collapse
|
21
|
Soudi S, Reinhold K, Engqvist L. Genetic architecture underlying host choice differentiation in the sympatric host races of Lochmaea capreae leaf beetles. Genetica 2016; 144:147-56. [PMID: 26857373 DOI: 10.1007/s10709-016-9885-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/25/2016] [Indexed: 10/22/2022]
Abstract
Speciation in herbivorous insects has received considerable attention during the last few decades. Much of this group's diversity originates from adaptive population divergence onto different host plants, which often involves the evolution of specialized patterns of host choice behaviour. Differences in host choice often translates directly into divergence in mating sites, and therefore positive assortative mating will be created which will act as a strong barrier to gene flow. In this study, we first explored whether host choice is a genetically determined trait in the sympatric willow and birch host races of the leaf feeding beetle Lochmaea capreae, or whether larval experience influences adult host choice. Once we had established that host choice is a genetically based trait we determined its genetic architecture. To achieve this, we employed a reciprocal transplant design in which offspring from pure willow and birch cross-types, F1, F2 and backcrosses were raised on each host plant and their preference was determined upon reaching adulthood. We then applied joint-scaling analysis to uncover the genetic architecture of host preference. Our results suggest that rearing host does not have a pronounced effect on adult's host choice; rather the segregation pattern implies the existence of genetic loci affecting host choice in these host races. The joint-scaling analysis revealed that population differences in host choice are mainly influenced by the contribution of additive genetic effects and also maternally inherited cytoplasmic effects. We explore the implications of our findings for evolutionary dynamics of sympatric host race formation and speciation.
Collapse
Affiliation(s)
- Shaghayegh Soudi
- Evolutionary Biology, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany.
| | - Klaus Reinhold
- Evolutionary Biology, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany
| | - Leif Engqvist
- Evolutionary Biology, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany.,Behavioural Ecology, Institute of Ecology and Evolution, University of Bern, 3032, Hinterkappelen, Switzerland
| |
Collapse
|
22
|
Soudi S, Reinhold K, Engqvist L. Ecologically dependent and intrinsic genetic signatures of postzygotic isolation between sympatric host races of the leaf beetle Lochmaea capreae. Evolution 2016; 70:471-9. [PMID: 26882317 DOI: 10.1111/evo.12846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 12/09/2015] [Accepted: 12/18/2015] [Indexed: 11/29/2022]
Abstract
The fitness of hybrids might be compromised as a result of intrinsic isolation and/or because they fall between ecological niches due to their intermediate phenotypes ("extrinsic isolation"). Here, we present data from several crosses (parental crosses, F1, F2, and backcrosses) between the two host races of Lochmaea capreae on willow and birch to test for extrinsic isolation, intrinsic isolation, and environmentally dependent genetic incompatibilities. We employed a reciprocal transplant design in which offspring were raised on either host plant and their survival was recorded until adulthood. We also applied joint-scaling analysis to determine the genetic architecture of hybrid inviability. The relative fitness of the backcrosses switched between environments; furthermore, the additive genetic-environment interaction was detected as the strongest effect in our analysis. These results provide strong evidence that divergent natural selection has played a central role in the evolution of hybrid dysfunction between host races. Joint-scaling analysis detected significant negative epistatic effects that are most evident in the poor performance of F2-hybrids on willow, indicating signs of intrinsic isolation. We did not find any evidence that genetic incompatibilities are manifested independently of environmental conditions. Our findings suggest the outcome of natural hybridization between these host races is mainly affected by extrinsic isolation and a weak contribution of intrinsic isolation.
Collapse
Affiliation(s)
- Shaghayegh Soudi
- Evolutionary Biology; Bielefeld University; D-33615 Bielefeld Germany
| | - Klaus Reinhold
- Evolutionary Biology; Bielefeld University; D-33615 Bielefeld Germany
| | - Leif Engqvist
- Evolutionary Biology; Bielefeld University; D-33615 Bielefeld Germany
- Behavioural Ecology, Institute of Ecology and Evolution; University of Bern; CH-3032 Hinterkappelen Switzerland
| |
Collapse
|
23
|
Havird JC, Whitehill NS, Snow CD, Sloan DB. Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution. Evolution 2015; 69:3069-81. [PMID: 26514987 DOI: 10.1111/evo.12808] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 12/11/2022]
Abstract
Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523.
| | - Nicholas S Whitehill
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, 80523
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523.
| |
Collapse
|
24
|
Zhang J, Ruhlman TA, Sabir J, Blazier JC, Jansen RK. Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae. THE PLANT CELL 2015; 27:563-73. [PMID: 25724640 PMCID: PMC4558654 DOI: 10.1105/tpc.114.134353] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/28/2015] [Accepted: 02/12/2015] [Indexed: 05/08/2023]
Abstract
Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae.
Collapse
Affiliation(s)
- Jin Zhang
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Jamal Sabir
- Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - J Chris Blazier
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin, Texas 78712 Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
25
|
Sloan DB. Using plants to elucidate the mechanisms of cytonuclear co-evolution. THE NEW PHYTOLOGIST 2015; 205:1040-6. [PMID: 25729802 DOI: 10.1111/nph.12835] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The presence of both cytoplasmic and nuclear genomes within eukaryotic cells raises fascinating questions about co-evolution between genomic compartments that experience fundamentally different mutation rates and modes of inheritance. The highly mutagenic environments found in the mitochondria of some eukaryotes have generated interest in the role that mitochondrial mutation accumulation plays in phenomena such as intracellular gene transfer, compensatory evolution in the nucleus and the evolution of reproductive isolation. Although plant systems have played an important historical role in the study of cytonuclear co-evolution, they remain underutilized in many respects. In particular, the enormous natural variation in DNA substitution rates, gene content and genome architecture in plant mitochondria - much of which has even been found within a single genus – provides opportunities to resolve longstanding evolutionary questions about the consequences of mitochondrial mutation accumulation. This review summarizes some of the classic questions about cytonuclear co-evolution that could be addressed by taking advantage of the variation in plants and highlights a recent analysis of the effect of mitochondrial mutation accumulation on rates of molecular evolution in the nucleus.
Collapse
|
26
|
Aledo JC, Valverde H, Ruíz-Camacho M, Morilla I, López FD. Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force. Genome Biol Evol 2014; 6:3064-76. [PMID: 25359921 PMCID: PMC4255772 DOI: 10.1093/gbe/evu240] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Respiratory complexes are encoded by two genomes (mitochondrial DNA [mtDNA] and nuclear DNA [nDNA]). Although the importance of intergenomic coadaptation is acknowledged, the forces and constraints shaping such coevolution are largely unknown. Previous works using cytochrome c oxidase (COX) as a model enzyme have led to the so-called “optimizing interaction” hypothesis. According to this view, mtDNA-encoded residues close to nDNA-encoded residues evolve faster than the rest of positions, favoring the optimization of protein–protein interfaces. Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the “optimizing hypothesis.” Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts. Nevertheless, noncontact residues from the surface of COX I subunit are a remarkable exception, being subjected to an exceptionally high purifying selection that may be related to the maintenance of a suitable heme environment. We also report that mtDNA-encoded residues involved in contacts with other mtDNA-encoded subunits are more constrained than mtDNA-encoded residues interacting with nDNA-encoded polypeptides. This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes. Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.
Collapse
Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Héctor Valverde
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Manuel Ruíz-Camacho
- Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Ian Morilla
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Spain
| | - Francisco Demetrio López
- Departamento de Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de Málaga, Spain
| |
Collapse
|
27
|
Ivankov DN, Finkelstein AV, Kondrashov FA. A structural perspective of compensatory evolution. Curr Opin Struct Biol 2014; 26:104-12. [PMID: 24981969 PMCID: PMC4141909 DOI: 10.1016/j.sbi.2014.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/11/2014] [Accepted: 05/16/2014] [Indexed: 11/25/2022]
Abstract
The study of molecular evolution is important because it reveals how protein functions emerge and evolve. Recently, several types of studies indicated that substitutions in molecular evolution occur in a compensatory manner, whereby the occurrence of a substitution depends on the amino acid residues at other sites. However, a molecular or structural basis behind the compensation often remains obscure. Here, we review studies on the interface of structural biology and molecular evolution that revealed novel aspects of compensatory evolution. In many cases structural studies benefit from evolutionary data while structural data often add a functional dimension to the study of molecular evolution.
Collapse
Affiliation(s)
- Dmitry N Ivankov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia
| | - Alexei V Finkelstein
- Laboratory of Protein Physics, Institute of Protein Research of the Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russia
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, 08010 Barcelona, Spain.
| |
Collapse
|
28
|
Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC. The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression. Genome Biol Evol 2014; 6:886-96. [PMID: 24696399 PMCID: PMC4007550 DOI: 10.1093/gbe/evu059] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 12/21/2022] Open
Abstract
Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive.
Collapse
Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
| | - Joana Vilela
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
| | - Miguel M. Fonseca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Spain
| | - Rute R. da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal
| | - Pierre Boursot
- Institut des Sciences de l’Evolution, Université Montpellier 2, CNRS, IRD, France
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO Laboratório Associado, Portugal
- Departamento de Biologia da Faculdade de Ciências da Universidade do Porto, Portugal
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula
| |
Collapse
|
29
|
Sloan DB, Triant DA, Wu M, Taylor DR. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol 2013; 31:673-82. [PMID: 24336923 DOI: 10.1093/molbev/mst259] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many mitochondrial and plastid protein complexes contain subunits that are encoded in different genomes. In animals, nuclear-encoded mitochondrial proteins often exhibit rapid sequence evolution, which has been hypothesized to result from selection for mutations that compensate for changes in interacting subunits encoded in mutation-prone animal mitochondrial DNA. To test this hypothesis, we analyzed nuclear genes encoding cytosolic and organelle ribosomal proteins in flowering plants. The model angiosperm genus Arabidopsis exhibits low organelle mutation rates, typical of most plants. Nevertheless, we found that (nuclear-encoded) subunits of organelle ribosomes in Arabidopsis have higher amino acid sequence polymorphism and divergence than their counterparts in cytosolic ribosomes, suggesting that organelle ribosomes experience relaxed functional constraint. However, the observed difference between organelle and cytosolic ribosomes was smaller than in animals and could be partially attributed to rapid evolution in N-terminal organelle-targeting peptides that are not involved in ribosome function. To test the role of organelle mutation more directly, we used transcriptomic data from an angiosperm genus (Silene) with highly variable rates of organelle genome evolution. We found that Silene species with unusually fast-evolving mitochondrial and plastid DNA exhibited increased amino acid sequence divergence in ribosomal proteins targeted to the organelles but not in those that function in cytosolic ribosomes. Overall, these findings support the hypothesis that rapid organelle genome evolution has selected for compensatory mutations in nuclear-encoded proteins. We conclude that coevolution between interacting subunits encoded in different genomic compartments within the eukaryotic cell is an important determinant of variation in rates of protein sequence evolution.
Collapse
|
30
|
Joseph B, Corwin JA, Li B, Atwell S, Kliebenstein DJ. Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome. eLife 2013; 2:e00776. [PMID: 24150750 PMCID: PMC3791467 DOI: 10.7554/elife.00776] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 09/03/2013] [Indexed: 12/30/2022] Open
Abstract
Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural variation. DOI: http://dx.doi.org/10.7554/eLife.00776.001.
Collapse
Affiliation(s)
- Bindu Joseph
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Jason A Corwin
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Suzi Atwell
- Department of Plant Sciences, University of California, Davis, Davis, United States
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, United States
- DynaMo Center of Excellence, University of Copenhagen, Frederiksberg, Denmark
| |
Collapse
|
31
|
Foley BR, Rose CG, Rundle DE, Leong W, Edmands S. Postzygotic isolation involves strong mitochondrial and sex-specific effects in Tigriopus californicus, a species lacking heteromorphic sex chromosomes. Heredity (Edinb) 2013; 111:391-401. [PMID: 23860232 DOI: 10.1038/hdy.2013.61] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 11/09/2022] Open
Abstract
Detailed studies of the genetics of speciation have focused on a few model systems, particularly Drosophila. The copepod Tigriopus californicus offers an alternative that differs from standard animal models in that it lacks heteromorphic chromosomes (instead, sex determination is polygenic) and has reduced opportunities for sexual conflict, because females mate only once. Quantitative trait loci (QTL) mapping was conducted on reciprocal F2 hybrids between two strongly differentiated populations, using a saturated linkage map spanning all 12 autosomes and the mitochondrion. By comparing sexes, a possible sex ratio distorter was found but no sex chromosomes. Although studies of standard models often find an excess of hybrid male sterility factors, we found no QTL for sterility and multiple QTL for hybrid viability (indicated by non-Mendelian adult ratios) and other characters. Viability problems were found to be stronger in males, but the usual explanations for weaker hybrid males (sex chromosomes, sensitivity of spermatogenesis, sexual selection) cannot fully account for these male viability problems. Instead, higher metabolic rates may amplify deleterious effects in males. Although many studies of standard speciation models find the strongest genetic incompatibilities to be nuclear-nuclear (specifically X chromosome-autosome), we found the strongest deleterious interaction in this system was mito-nuclear. Consistent with the snowball theory of incompatibility accumulation, we found that trigenic interactions in this highly divergent cross were substantially more frequent (>6×) than digenic interactions. This alternative system thus allows important comparisons to studies of the genetics of reproductive isolation in more standard model systems.
Collapse
Affiliation(s)
- B R Foley
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | | | | | | | | |
Collapse
|
32
|
Willett CS. Gene conversion yields novel gene combinations in paralogs of GOT1 in the copepod Tigriopus californicus. BMC Evol Biol 2013; 13:148. [PMID: 23845062 PMCID: PMC3728101 DOI: 10.1186/1471-2148-13-148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/08/2013] [Indexed: 11/24/2022] Open
Abstract
Background Gene conversion of duplicated genes can slow the divergence of paralogous copies over time but can also result in other interesting evolutionary patterns. Islands of genetic divergence that persist in the face of gene conversion can point to gene regions undergoing selection for new functions. Novel combinations of genetic variation that differ greatly from the original sequence can result from the transfer of genetic variation between paralogous genes by rare gene conversion events. Genetically divergent populations of the copepod Tigriopus californicus provide an excellent model to look at the patterns of divergence among paralogs across multiple independent evolutionary lineages. Results In this study the evolution of a set of paralogous genes encoding putative aspartate transaminase proteins (called GOT1 here) are examined in populations of the copepod T. californicus. One pair of duplicated genes, GOT1p1 and GOT1p2, has regions of high divergence between the copies in the face of apparent on-going gene conversion. The GOT1p2 gene also has unique haplotypes in two populations that appear to have resulted from a transfer of genetic variation via inter-paralog gene conversion. A second pair of duplicated genes GOT1Sr and GOT1Sd also shows evidence of gene conversion, but this gene conversion does not appear to have maintained each as a functional copy in all populations. Conclusions The patterns of conservation and sequence divergence across this set of paralogous genes among populations of T. californicus suggest that some interesting evolutionary patterns are occurring at these loci. The results for the GOT1p1/GOT1p2 paralogs illustrate how gene conversion can factor in the creation of a mosaic pattern of regions of high divergence and low divergence. When coupled with rare gene conversion events of divergent regions, this pattern can result in the formation of novel proteins differing substantially from either original protein. The evolutionary patterns across these paralogs show how gene conversion can both constrain and facilitate diversification of genetic sequences.
Collapse
Affiliation(s)
- Christopher S Willett
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| |
Collapse
|
33
|
Wang HY, Hsieh CH, Huang CG, Kong SW, Chang HC, Lee HH, Wang WK, Chen SL, Tzeng HY, Wu WJ. Genetic and physiological data suggest demographic and adaptive responses in complex interactions between populations of figs (Ficus pumila) and their pollinating wasps (Wiebesia pumilae). Mol Ecol 2013; 22:3814-32. [DOI: 10.1111/mec.12336] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 03/14/2013] [Accepted: 03/21/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Hurng-Yi Wang
- Graduate Institute of Clinical Medicine; National Taiwan University; Taipei 100 Taiwan
| | - Chia-Hung Hsieh
- Graduate Institute of Clinical Medicine; National Taiwan University; Taipei 100 Taiwan
| | - Chin-Gi Huang
- Department of Entomology; National Taiwan University; Taipei 106 Taiwan
| | - Siu-Wah Kong
- Department of Entomology; National Taiwan University; Taipei 106 Taiwan
| | - Hsiao-Chi Chang
- Graduate Institute of Clinical Medicine; National Taiwan University; Taipei 100 Taiwan
| | - Ho-Huei Lee
- Department of Entomology; National Taiwan University; Taipei 106 Taiwan
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science; Feng Chia University; Taichung 407 Taiwan
| | - Shih-Lun Chen
- Graduate Institute of Clinical Medicine; National Taiwan University; Taipei 100 Taiwan
| | - Hsy-Yu Tzeng
- Department of Forestry; National Chung Hsing University; Taichung 402 Taiwan
| | - Wen-Jer Wu
- Department of Entomology; National Taiwan University; Taipei 106 Taiwan
- Research Center for Plant Medicine; National Taiwan University; Taipei 106 Taiwan
| |
Collapse
|
34
|
Watt WB. Specific-gene studies of evolutionary mechanisms in an age of genome-wide surveying. Ann N Y Acad Sci 2013; 1289:1-17. [PMID: 23679204 DOI: 10.1111/nyas.12139] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The molecular tools of genomics have great power to reveal patterns of genetic difference within or among species, but must be complemented by the mechanistic study of the genetic variants found if these variants' evolutionary meaning is to be well understood. Central to this purpose is knowledge of the organisms' genotype-phenotype-environment interactions, which embody biological adaptation and constraint and thus drive natural selection. The history of this approach is briefly reviewed. Strategies embracing the complementarity of genomics and specific-gene studies in evolution are considered. Implementation of these strategies, and examples showing their feasibility and power, are discussed. Initial generalizations emphasize: (1) reproducibility of adaptive mechanisms; (2) evolutionary co-importance of variation in protein sequences and expression; (3) refinement of rudimentary molecular functions as an origin of evolutionary innovations; (4) identification of specific-gene mechanisms as underpinnings of genomic or quantitative genetic variation; and (5) multiple forms of adaptive or constraining epistasis among genes. Progress along these lines will advance understanding of evolution and support its use in addressing urgent medical and environmental applications.
Collapse
Affiliation(s)
- Ward B Watt
- Department of Biology, Stanford University, Stanford, California and Rocky Mountain Biological Laboratory, Crested Butte, Colorado, USA.
| |
Collapse
|
35
|
Parmakelis A, Kotsakiozi P, Rand D. Animal mitochondria, positive selection and cyto-nuclear coevolution: insights from pulmonates. PLoS One 2013; 8:e61970. [PMID: 23620797 PMCID: PMC3631144 DOI: 10.1371/journal.pone.0061970] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 03/15/2013] [Indexed: 01/06/2023] Open
Abstract
Pulmonate snails have remarkably high levels of mtDNA polymorphism within species and divergence between species, making them an interesting group for the study of mutation and selection on mitochondrial genomes. The availability of sequence data from most major lineages – collected largely for studies of phylogeography - provides an opportunity to perform several tests of selection that may provide general insights into the evolutionary forces that have produced this unusual pattern. Several protein coding mtDNA datasets of pulmonates were analyzed towards this direction. Two different methods for the detection of positive selection were used, one based on phylogeny, and the other on the McDonald-Kreitman test. The cyto-nuclear coevolution hypothesis, often implicated to account for the high levels of mtDNA divergence of some organisms, was also addressed by assessing the divergence pattern exhibited by a nuclear gene. The McDonald-Kreitman test indicated multiple signs of positive selection in the mtDNA genes, but was significantly biased when sequence divergence was high. The phylogenetic method identified five mtDNA datasets as affected by positive selection. In the nuclear gene, the McDonald-Kreitman test provided no significant results, whereas the phylogenetic method identified positive selection as likely present. Overall, our findings indicate that: 1) slim support for the cyto-nuclear coevolution hypothesis is present, 2) the elevated rates of mtDNA polymorphims and divergence in pulmonates do not appear to be due to pervasive positive selection, 3) more stringent tests show that spurious positive selection is uncovered when distant taxa are compared and 4) there are significant examples of positive selection acting in some cases, so it appears that mtDNA evolution in pulmonates can escape from strict deleterious evolution suggested by the Muller’s ratchet effect.
Collapse
Affiliation(s)
- Aristeidis Parmakelis
- Department of Ecology and Taxonomy, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
| | | | | |
Collapse
|
36
|
Pichaud N, Ballard JWO, Tanguay RM, Blier PU. Mitochondrial haplotype divergences affect specific temperature sensitivity of mitochondrial respiration. J Bioenerg Biomembr 2012; 45:25-35. [DOI: 10.1007/s10863-012-9473-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
|
37
|
Burton RS, Barreto FS. A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities? Mol Ecol 2012; 21:4942-57. [PMID: 22994153 DOI: 10.1111/mec.12006] [Citation(s) in RCA: 221] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/18/2012] [Accepted: 07/25/2012] [Indexed: 01/07/2023]
Abstract
Evolution in allopatric populations can lead to incompatibilities that result in reduced hybrid fitness and ultimately reproductive isolation upon secondary contact. The Dobzhansky-Muller (DM) model nicely accounts for the evolution of such incompatibilities. Although DM incompatibilities were originally conceived as resulting of interactions between nuclear genes, recent studies have documented cases where incompatibilities have arisen between nuclear and mitochondrial genomes (mtDNA). Although mtDNA comprises only a tiny component (typically <<0.01%) of an organism's genetic material, several features of mtDNA may lead to a disproportionate contribution to the evolution of hybrid incompatibilities: (i) essentially all functions of mtDNA require interaction with nuclear gene products. All mtDNA-encoded proteins are components of the oxidative phosphorylation (OXPHOS) system and all mtDNA-encoded RNAs are part of the mitochondrial protein synthetic machinery; both processes require interaction with nuclear-encoded proteins for function. (ii) Transcription and replication of mtDNA also involve mitonuclear interactions as nuclear-encoded proteins must bind to regulatory motifs in the mtDNA to initiate these processes. (iii) Although features of mtDNA vary amongst taxa, metazoan mtDNA is typically characterized by high nucleotide substitution rates, lack of recombination and reduced effective population sizes that collectively lead to increased chance fixation of mildly deleterious mutations. Combined, these features create an evolutionary dynamic where rapid mtDNA evolution favours compensatory nuclear gene evolution, ultimately leading to co-adaptation of mitochondrial and nuclear genomes. When previously isolated lineages hybridize in nature or in the lab, intergenomic co-adaptation is disrupted and hybrid breakdown is observed; the role of intergenomic co-adaptation in hybrid breakdown and speciation will generally be most pronounced when rates of mtDNA evolution are high or when restricted gene flow results in significant population differentiation.
Collapse
Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
| | | |
Collapse
|
38
|
Hicks KA, Howe DK, Leung A, Denver DR, Estes S. In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae. PLoS One 2012; 7:e43837. [PMID: 22952781 PMCID: PMC3429487 DOI: 10.1371/journal.pone.0043837] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/30/2012] [Indexed: 12/18/2022] Open
Abstract
We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.
Collapse
Affiliation(s)
- Kiley A. Hicks
- Biology Department, Portland State University, Portland, Oregon, United States of America
| | - Dana K. Howe
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Aubrey Leung
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Dee R. Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Suzanne Estes
- Biology Department, Portland State University, Portland, Oregon, United States of America
- * E-mail:
| |
Collapse
|
39
|
Abstract
Phenotypes relevant to oxidative phosphorylation (OXPHOS) in eukaryotes are jointly determined by nuclear and mitochondrial DNA (mtDNA). Thus, in humans, the variable clinical presentations of mitochondrial disease patients bearing the same primary mutation, whether in nuclear or mitochondrial DNA, have been attributed to putative genetic determinants carried in the “other” genome, though their identity and the molecular mechanism(s) by which they might act remain elusive. Here we demonstrate cytoplasmic suppression of the mitochondrial disease-like phenotype of the Drosophila melanogaster nuclear mutant tko25t, which includes developmental delay, seizure sensitivity, and defective male courtship. The tko25t strain carries a mutation in a mitoribosomal protein gene, causing OXPHOS deficiency due to defective intramitochondrial protein synthesis. Phenotypic suppression was associated with increased mtDNA copy number and increased mitochondrial biogenesis, as measured by the expression levels of porin voltage dependent anion channel and Spargel (PGC1α). Ubiquitous overexpression of Spargel in tko25t flies phenocopied the suppressor, identifying it as a key mechanistic target thereof. Suppressor-strain mtDNAs differed from related nonsuppressor strain mtDNAs by several coding-region polymorphisms and by length and sequence variation in the noncoding region (NCR), in which the origin of mtDNA replication is located. Cytoplasm from four of five originally Wolbachia-infected strains showed the same suppressor effect, whereas that from neither of two uninfected strains did so, suggesting that the stress of chronic Wolbachia infection may provide evolutionary selection for improved mitochondrial fitness under metabolic stress. Our findings provide a paradigm for understanding the role of mtDNA genotype in human disease.
Collapse
|
40
|
Quantifying the Elevation of Mitochondrial DNA Evolutionary Substitution Rates Over Nuclear Rates in the Intertidal Copepod Tigriopus californicus. J Mol Evol 2012; 74:310-8. [DOI: 10.1007/s00239-012-9508-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
|
41
|
Davies R, Mathers KE, Hume AD, Bremer K, Wang Y, Moyes CD. Hybridization in Sunfish Influences the Muscle Metabolic Phenotype. Physiol Biochem Zool 2012; 85:321-31. [DOI: 10.1086/666058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
42
|
Pichaud N, Ballard JWO, Tanguay RM, Blier PU. Naturally occurring mitochondrial DNA haplotypes exhibit metabolic differences: insight into functional properties of mitochondria. Evolution 2012; 66:3189-97. [PMID: 23025608 DOI: 10.1111/j.1558-5646.2012.01683.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Linking the mitochondrial genotype and the organismal phenotype is of paramount importance in evolution of mitochondria. In this study, we determined the differences in catalytic properties of mitochondria dictated by divergences in the siII and siIII haplogroups of Drosophila simulans using introgressions of siII mtDNA type into the siIII nuclear background. We used a novel in situ method (permeabilized fibers) that allowed us to accurately measure the consumption of oxygen by mitochondria in constructed siII-introgressed flies and in siIII-control flies. Our results showed that the catalytic capacity of the electron transport system is not impaired by introgressions, suggesting that the functional properties of mitochondria are tightly related to the mtDNA haplogroup and not to the nuclear DNA or to the mito-nuclear interactions. This is the first study, to our knowledge, that demonstrates a naturally occurring haplogroup can confer specific functional differences in aspects of mitochondrial metabolism. This study illustrates the importance of mtDNA changes on organelle evolution and highlights the potential bioenergetic and metabolic impacts that divergent mitochondrial haplogroups may have upon a wide variety of species including humans.
Collapse
Affiliation(s)
- Nicolas Pichaud
- Laboratoire de biologie intégrative, Département de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Québec, Canada G5L 3A1.
| | | | | | | |
Collapse
|
43
|
Gagnaire PA, Normandeau E, Bernatchez L. Comparative Genomics Reveals Adaptive Protein Evolution and a Possible Cytonuclear Incompatibility between European and American Eels. Mol Biol Evol 2012; 29:2909-19. [DOI: 10.1093/molbev/mss076] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
44
|
Pierron D, Wildman DE, Hüttemann M, Letellier T, Grossman LI. Evolution of the couple cytochrome c and cytochrome c oxidase in primates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 748:185-213. [PMID: 22729859 DOI: 10.1007/978-1-4614-3573-0_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondrial energy metabolism has been affected by a broad set of ancient and recent evolutionary events. The oldest example is the endosymbiosis theory that led to mitochondria and a recently proposed example is adaptation to cold climate by anatomically modern human lineages. Mitochondrial energy metabolism has also been associated with an important area in anthropology and evolutionary biology, brain enlargement in human evolution. Indeed, several studies have pointed to the need for a major metabolic rearrangement to supply a sufficient amount of energy for brain development in primates.The genes encoding for the coupled cytochrome c (Cyt c) and cytochrome c oxidase (COX, complex IV, EC 1.9.3.1) seem to have an exceptional pattern of evolution in the anthropoid lineage. It has been proposed that this evolution was linked to the rearrangement of energy metabolism needed for brain enlargement. This hypothesis is reinforced by the fact that the COX enzyme was proposed to have a large role in control of the respiratory chain and thereby global energy production.After summarizing major events that occurred during the evolution of COX and cytochrome c on the primate lineage, we review the different evolutionary forces that could have influenced primate COX evolution and discuss the probable causes and consequences of this evolution. Finally, we discuss and review the co-occurring primate phenotypic evolution.
Collapse
Affiliation(s)
- Denis Pierron
- Wayne State University School of Medicine, Detroit, MI 48201, USA
| | | | | | | | | |
Collapse
|
45
|
Affiliation(s)
- I Keller
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Seestrasse 79, CH-6047 Kastanienbaum, Switzerland.
| | | |
Collapse
|
46
|
Willett CS. Hybrid breakdown weakens under thermal stress in population crosses of the copepod Tigriopus californicus. ACTA ACUST UNITED AC 2011; 103:103-14. [PMID: 22016434 DOI: 10.1093/jhered/esr109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The outcome of hybridization can be impacted by environmental conditions, which themselves can contribute to reproductive isolation between taxa. In crosses of genetically divergent populations, hybridization can have both negative and positive impacts on fitness, the balance between which might be tipped by changes in the environment. Genetically divergent populations of the intertidal copepod Tigriopus californicus have been shown to differ in thermal tolerance at high temperatures along a latitudinal gradient. In this study, a series of crosses were made between pairs of genetically divergent populations of T. californicus, and the thermal tolerance of these hybrids was tested. In most cases, the first-generation hybrids had relatively high thermal tolerance and the second-generation hybrids were not generally reduced below the less-tolerant parental population for high temperature tolerance. This pattern contrasts with previous studies from crosses of genetically divergent populations of this copepod, which often shows hybrid breakdown in these second-generation hybrids for other measures of fitness. These results suggest that high temperature stress could either increase the positive impacts of hybridization or decrease the negative impacts of hybridization resulting in lowered hybrid breakdown in these population crosses.
Collapse
Affiliation(s)
- Christopher S Willett
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| |
Collapse
|
47
|
Complex deleterious interactions associated with malic enzyme may contribute to reproductive isolation in the copepod Tigriopus californicus. PLoS One 2011; 6:e21177. [PMID: 21731664 PMCID: PMC3120845 DOI: 10.1371/journal.pone.0021177] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 05/22/2011] [Indexed: 11/24/2022] Open
Abstract
Dobzhansky-Muller incompatibilities can result from the interactions of more than a single pair of interacting genes and there are several different models of how such complex interactions can be structured. Previous empirical work has identified complex conspecific epistasis as a form of complex interaction that has contributed to postzygotic reproductive isolation between taxa, but other forms of complexity are also possible. Here, I probe the genetic basis of reproductive isolation in crosses of the intertidal copepod Tigriopus californicus by looking at the impact of markers in genes encoding metabolic enzymes in F2 hybrids. The region of the genome associated with the locus ME2 is shown to have strong, repeatable impacts on the fitness of hybrids in crosses and epistatic interactions with another chromosomal region marked by the GOT2 locus in one set of crosses. In a cross between one of these populations and a third population, these two regions do not appear to interact despite the continuation of a large effect of the ME2 region itself in both crosses. The combined results suggest that the ME2 chromosomal region is involved in incompatibilities with several unique partners. If these deleterious interactions all stem from the same factor in this region, that would suggest a different form of complexity from complex conspecific epistasis, namely, multiple independent deleterious interactions stemming from the same factor. Confirmation of this idea will require more fine-scale mapping of the interactions of the ME2 region of the genome.
Collapse
|
48
|
Pritchard VL, Dimond L, Harrison JS, S Velázquez CC, Zieba JT, Burton RS, Edmands S. Interpopulation hybridization results in widespread viability selection across the genome in Tigriopus californicus. BMC Genet 2011; 12:54. [PMID: 21639918 PMCID: PMC3138442 DOI: 10.1186/1471-2156-12-54] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 06/03/2011] [Indexed: 11/10/2022] Open
Abstract
Background Genetic interactions within hybrids influence their overall fitness. Understanding the details of these interactions can improve our understanding of speciation. One experimental approach is to investigate deviations from Mendelian expectations (segregation distortion) in the inheritance of mapped genetic markers. In this study, we used the copepod Tigriopus californicus, a species which exhibits high genetic divergence between populations and a general pattern of reduced fitness in F2 interpopulation hybrids. Previous studies have implicated both nuclear-cytoplasmic and nuclear-nuclear interactions in causing this fitness reduction. We identified and mapped population-diagnostic single nucleotide polymorphisms (SNPs) and used these to examine segregation distortion across the genome within F2 hybrids. Results We generated a linkage map which included 45 newly elucidated SNPs and 8 population-diagnostic microsatellites used in previous studies. The map, the first available for the Copepoda, was estimated to cover 75% of the genome and included markers on all 12 T. californicus chromosomes. We observed little segregation distortion in newly hatched F2 hybrid larvae (fewer than 10% of markers at p < 0.05), but strikingly higher distortion in F2 hybrid adult males (45% of markers at p < 0.05). Hence, segregation distortion was primarily caused by selection against particular genetic combinations which acted between hatching and maturity. Distorted markers were not distributed randomly across the genome but clustered on particular chromosomes. In contrast to other studies in this species we found little evidence for cytonuclear coadaptation. Instead, different linkage groups exhibited markedly different patterns of distortion, which appear to have been influenced by nuclear-nuclear epistatic interactions and may also reflect genetic load carried within the parental lines. Conclusion Adult male F2 hybrids between two populations of T. californius exhibit dramatic segregation distortion across the genome. Distorted loci are clustered within specific linkage groups, and the direction of distortion differs between chromosomes. This segregation distortion is due to selection acting between hatching and adulthood.
Collapse
Affiliation(s)
- Victoria L Pritchard
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, USA.
| | | | | | | | | | | | | |
Collapse
|
49
|
Kartavtsev YP. Sequence divergence at mitochondrial genes in animals: Applicability of DNA data in genetics of speciation and molecular phylogenetics. Mar Genomics 2011; 4:71-81. [DOI: 10.1016/j.margen.2011.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 01/26/2011] [Accepted: 02/23/2011] [Indexed: 11/15/2022]
|
50
|
Eytan RI, Hellberg ME. Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes. Evolution 2011; 64:3380-97. [PMID: 20584072 DOI: 10.1111/j.1558-5646.2010.01071.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species' Caribbean ranges. Although both species shared a similar pattern of genetic subdivision, A. spinosa had 20-25 times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fish.
Collapse
Affiliation(s)
- Ron I Eytan
- Department of Biological Sciences, 107 Life Sciences Building, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
| | | |
Collapse
|