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Healy TM, Burton RS. Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence. Evolution 2023; 77:2100-2108. [PMID: 37407024 DOI: 10.1093/evolut/qpad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.
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Affiliation(s)
- Timothy M Healy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California-San Diego, La Jolla, CA, United States
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Pereira RJ, Lima TG, Pierce-Ward NT, Chao L, Burton RS. Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities. Mol Ecol 2021; 30:6403-6416. [PMID: 34003535 DOI: 10.1111/mec.15985] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/29/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genomic background, causing inviability, sterility or other forms of low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids of the copepod Tigriopus californicus, in which frequencies of compatible and incompatible nuclear alleles change in response to an alternative mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across three replicates of each reciprocal cross, but markedly different patterns between mitochondrial backgrounds. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome showed allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. In 87% and 89% of these genomic regions, the dominant nuclear allele matched the associated mitochondrial background, consistent with mitonuclear co-adaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome-wide barriers to gene flow between closely related taxa.
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Affiliation(s)
- Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thiago G Lima
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - N Tessa Pierce-Ward
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lin Chao
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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Han KL, Barreto FS. Pervasive Mitonuclear Coadaptation Underlies Fast Development in Interpopulation Hybrids of a Marine Crustacean. Genome Biol Evol 2021; 13:6121088. [PMID: 33502469 PMCID: PMC7947751 DOI: 10.1093/gbe/evab004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Cellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in multiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F2 hybrids between two divergent populations of the copepod Tigriopus californicus to examine mitonuclear coadaptation across the nuclear genome. Using developmental rate as a measure of fitness, we found that fast-developing copepods had higher ATP synthesis capacity than slow developers, suggesting variation in developmental rates is at least partly associated with mitochondrial dysfunction. Using Pool-seq, we detected strong biases for maternal alleles across 7 (of 12) chromosomes in both reciprocal crosses in high-fitness hybrids, whereas low-fitness hybrids showed shifts toward the paternal population. Comparison with previous results on a different hybrid cross revealed largely different patterns of strong mitonuclear coadaptation associated with developmental rate. Our findings suggest that functional coadaptation between interacting nuclear and mitochondrial components is reflected in strong polygenic effects on this life-history phenotype, and reveal that molecular coadaptation follows independent evolutionary trajectories among isolated populations.
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Affiliation(s)
- Kin-Lan Han
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA.,Department of Biology, University of Washington, Seattle, Washington, USA
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
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Strong selective effects of mitochondrial DNA on the nuclear genome. Proc Natl Acad Sci U S A 2020; 117:6616-6621. [PMID: 32156736 DOI: 10.1073/pnas.1910141117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod Tigriopus californicus to disrupt putatively coevolved mitonuclear genotypes in reciprocal F2 hybrids. We utilized interindividual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and in vitro ATP synthesis rates of mitochondria isolated from high-fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low-fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high- or low-fitness hybrids. Significant biases for maternal alleles were detected on 5 (of 12) chromosomes in high-fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low-fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that intergenomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.
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Doyle JM, Willoughby JR, Bell DA, Bloom PH, Bragin EA, Fernandez NB, Katzner TE, Leonard K, DeWoody JA. Elevated Heterozygosity in Adults Relative to Juveniles Provides Evidence of Viability Selection on Eagles and Falcons. J Hered 2019; 110:696-706. [DOI: 10.1093/jhered/esz048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/01/2019] [Indexed: 02/06/2023] Open
Abstract
AbstractViability selection yields adult populations that are more genetically variable than those of juveniles, producing a positive correlation between heterozygosity and survival. Viability selection could be the result of decreased heterozygosity across many loci in inbred individuals and a subsequent decrease in survivorship resulting from the expression of the deleterious alleles. Alternatively, locus-specific differences in genetic variability between adults and juveniles may be driven by forms of balancing selection, including heterozygote advantage, frequency-dependent selection, or selection across temporal and spatial scales. We use a pooled-sequencing approach to compare genome-wide and locus-specific genetic variability between 74 golden eagle (Aquila chrysaetos), 62 imperial eagle (Aquila heliaca), and 69 prairie falcon (Falco mexicanus) juveniles and adults. Although genome-wide genetic variability is comparable between juvenile and adult golden eagles and prairie falcons, imperial eagle adults are significantly more heterozygous than juveniles. This evidence of viability selection may stem from a relatively smaller imperial eagle effective population size and potentially greater genetic load. We additionally identify ~2000 single-nucleotide polymorphisms across the 3 species with extreme differences in heterozygosity between juveniles and adults. Many of these markers are associated with genes implicated in immune function or olfaction. These loci represent potential targets for studies of how heterozygote advantage, frequency-dependent selection, and selection over spatial and temporal scales influence survivorship in avian species. Overall, our genome-wide data extend previous studies that used allozyme or microsatellite markers and indicate that viability selection may be a more common evolutionary phenomenon than often appreciated.
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Affiliation(s)
- Jacqueline M Doyle
- Department of Biological Sciences, Towson University, Baltimore, MD
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
| | - Janna R Willoughby
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, Alabama
- Department of Biological Sciences, Purdue University, West Lafayette, IN
| | - Douglas A Bell
- Department of Biological Sciences, Towson University, Baltimore, MD
- East Bay Regional Park District, Oakland, CA
- Department of Ornithology and Mammalogy, California Academy of Sciences, San Francisco, CA
| | - Peter H Bloom
- Department of Biological Sciences, Towson University, Baltimore, MD
- Bloom Research Inc., Los Angeles, CA
| | - Evgeny A Bragin
- Department of Biological Sciences, Towson University, Baltimore, MD
- Faculty of Natural Science, Kostanay State Pedagogical University, Kostanay, Kazakhstan
- The Peregrine Fund, Boise, ID
- Science Department, Naurzum National Nature Reserve, Kostanay Oblast, Naurzumski Raijon, Karamendy, Kazakhstan
| | - Nadia B Fernandez
- Department of Biological Sciences, Towson University, Baltimore, MD
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA
| | - Todd E Katzner
- Department of Biological Sciences, Towson University, Baltimore, MD
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID
| | - Kolbe Leonard
- Department of Biological Sciences, Towson University, Baltimore, MD
- Department of Computer and Information Sciences, Towson University, Baltimore, MD
| | - J Andrew DeWoody
- Department of Biological Sciences, Towson University, Baltimore, MD
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
- Department of Biological Sciences, Purdue University, West Lafayette, IN
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Dorant Y, Benestan L, Rougemont Q, Normandeau E, Boyle B, Rochette R, Bernatchez L. Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus) as a case study. Ecol Evol 2019; 9:6606-6623. [PMID: 31236247 PMCID: PMC6580275 DOI: 10.1002/ece3.5240] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost-effective sequencing approaches, namely Pool-seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping-by-sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool-seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool-seq data showed F ST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar F ST estimates, indicating that individual-based approaches provided more congruent results than Pool-seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost-effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.
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Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Pêches et Océans CanadaInstitut Maurice‐LamontagneMont‐JoliCanada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Plateforme d'analyses génomiques, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Rémy Rochette
- Department of BiologyUniversity of New BrunswickSaint JohnCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
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