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1
Snoek, L. Basten, Helen E. Orbidans, Jana J. Stastna, Aafke Aartse, Miriam Rodriguez, Joost A. G. Riksen, Jan E. Kammenga, and Simon C. Harvey. "Widespread Genomic Incompatibilities inCaenorhabditis elegans." G3: Genes|Genomes|Genetics 4, no. 10 (August 15, 2014): 1813–23. http://dx.doi.org/10.1534/g3.114.013151.
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Birchler, James A., and Reiner A. Veitia. "Genomic Balance and Speciation." Epigenetics Insights 12 (January 2019): 251686571984029. http://dx.doi.org/10.1177/2516865719840291.
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The role of genomic balance in accumulating species hybrid incompatibilities is discussed. Aneuploidy has been shown to produce more global modulations than polyploidy with the responsible genes being transcription factors and signaling components involved in molecular complexes, illustrating a stoichiometric component to gene expression. Genomic imbalance is usually detrimental to the organism and in many cases results in lethality. Here, it is proposed that once gene flow is prevented between or within populations by various speciation initiating processes, the stoichiometric relationship of members of macromolecular complexes can change via compensatory drift with the eventual result of newly established functional balances. However, when these new relationships are brought together in interspecific hybrids, detrimental consequences will occur. We suggest that these detrimental interactions contribute to hybrid incompatibilities.
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Ohta, Naoyuki, Nicole Kaplan, James Tyler Ng, Basile Jules Gravez, and Lionel Christiaen. "Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis." G3: Genes|Genomes|Genetics 10, no. 8 (June 9, 2020): 2697–711. http://dx.doi.org/10.1534/g3.120.401427.
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Reproductive isolation is central to speciation, but interspecific crosses between two closely related species can produce viable and fertile hybrids. Two different species of tunicates in the same ascidian genus, Ciona robusta and Ciona intestinalis, can produce hybrids. However, wild sympatric populations display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took advantage of a closed culture system to cross C. robusta with C. intestinalis and established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation to characterize the genetic basis of simple traits, and further probe the physiological mechanisms underlying reproductive isolation. Partial viability of first and second generation hybrids suggested that both pre- and postzygotic mechanisms contributed to genomic incompatibilities in hybrids. We observed asymmetric fitness, whereby the C. intestinalis maternal lines fared more poorly in our system, pointing to maternal origins of species-specific sensitivity. We discuss the possibility that asymmetrical second generation inviability and infertility emerge from interspecific incompatibilities between the nuclear and mitochondrial genomes, or other maternal effect genes. This work paves the way to quantitative genetic approaches to study the mechanisms underlying genomic incompatibilities and other complex traits in the genome-enabled Ciona model.
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Liu, Shaojun, Jing Luo, Jing Chai, Li Ren, Yi Zhou, Feng Huang, Xiaochuan Liu, et al. "Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross." Proceedings of the National Academy of Sciences 113, no. 5 (January 14, 2016): 1327–32. http://dx.doi.org/10.1073/pnas.1512955113.
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Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF1. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF2 hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.
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Kinser, Taliesin J., Ronald D. Smith, Amelia H. Lawrence, Arielle M. Cooley, Mario Vallejo-Marín, Gregory D. Conradi Smith, and Joshua R. Puzey. "Endosperm-based incompatibilities in hybrid monkeyflowers." Plant Cell 33, no. 7 (April 25, 2021): 2235–57. http://dx.doi.org/10.1093/plcell/koab117.
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Abstract Endosperm is an angiosperm innovation central to their reproduction whose development, and thus seed viability, is controlled by genomic imprinting, where expression from certain genes is parent-specific. Unsuccessful imprinting has been linked to failed inter-specific and inter-ploidy hybridization. Despite their importance in plant speciation, the underlying mechanisms behind these endosperm-based barriers remain poorly understood. Here, we describe one such barrier between diploid Mimulus guttatus and tetraploid Mimulus luteus. The two parents differ in endosperm DNA methylation, expression dynamics, and imprinted genes. Hybrid seeds suffer from underdeveloped endosperm, reducing viability, or arrested endosperm and seed abortion when M. guttatus or M. luteus is seed parent, respectively, and transgressive methylation and expression patterns emerge. The two inherited M. luteus subgenomes, genetically distinct but epigenetically similar, are expressionally dominant over the M. guttatus genome in hybrid embryos and especially their endosperm, where paternal imprints are perturbed. In aborted seeds, de novo methylation is inhibited, potentially owing to incompatible paternal instructions of imbalanced dosage from M. guttatus imprints. We suggest that diverged epigenetic/regulatory landscapes between parental genomes induce epigenetic repatterning and global shifts in expression, which, in endosperm, may uniquely facilitate incompatible interactions between divergent imprinting schemes, potentially driving rapid barriers.
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McKenzie, Jessica L., Dillon J. Chung, Timothy M. Healy, Reid S. Brennan, Heather J. Bryant, Andrew Whitehead, and Patricia M. Schulte. "Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation." Integrative and Comparative Biology 59, no. 4 (July 8, 2019): 925–37. http://dx.doi.org/10.1093/icb/icz124.
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Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.
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Bomblies, Kirsten, and Detlef Weigel. "Arabidopsis and relatives as models for the study of genetic and genomic incompatibilities." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1547 (June 12, 2010): 1815–23. http://dx.doi.org/10.1098/rstb.2009.0304.
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The past few years have seen considerable advances in speciation research, but whether drift or adaptation is more likely to lead to genetic incompatibilities remains unknown. Some of the answers will probably come from not only studying incompatibilities between well-established species, but also from investigating incipient speciation events, to learn more about speciation as an evolutionary process. The genus Arabidopsis , which includes the widely used Arabidopsis thaliana , provides a useful set of model species for studying many aspects of population divergence. The genus contains both self-incompatible and incompatible species, providing a platform for studying the impact of mating system changes on genetic differentiation. Another important path to plant speciation is via formation of polyploids, and this can be investigated in the young allotetraploid species A. arenosa . Finally, there are many cases of intraspecific incompatibilities in A. thaliana , and recent progress has been made in discovering the genes underlying both F 1 and F 2 breakdown. In the near future, all these studies will be greatly empowered by complete genome sequences not only for all members of this relatively small genus, but also for many different individuals within each species.
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Dion-Côté, Anne-Marie, Radka Symonová, Petr Ráb, and Louis Bernatchez. "Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring." Proceedings of the Royal Society B: Biological Sciences 282, no. 1802 (March 7, 2015): 20142862. http://dx.doi.org/10.1098/rspb.2014.2862.
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Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish ( Coregonus clupeaformis ). We examined chromosomes in pure embryos, and healthy and malformed backcross embryos. While pure individuals displayed chromosome numbers corresponding to the expected diploid number (2 n = 80), healthy backcrosses showed evidence of mitotic instability through an increased variance of chromosome numbers within an individual. In malformed backcrosses, extensive aneuploidy corresponding to multiples of the haploid number (1 n = 40, 2 n = 80, 3 n = 120) was found, suggesting meiotic breakdown in their F 1 parent. However, no detectable chromosome rearrangements between parental forms were identified. Genomic instability through aneuploidy thus appears to contribute to reproductive isolation between dwarf and normal lake whitefish, despite their very recent divergence (approx. 15–20 000 generations). Our data suggest that genetic incompatibilities may accumulate early during speciation and limit hybridization between nascent species.
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Bourgeois, Yann, and Stéphane Boissinot. "On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements." Genes 10, no. 6 (May 30, 2019): 419. http://dx.doi.org/10.3390/genes10060419.
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Transposable elements (TEs) play an important role in shaping genomic organization and structure, and may cause dramatic changes in phenotypes. Despite the genetic load they may impose on their host and their importance in microevolutionary processes such as adaptation and speciation, the number of population genetics studies focused on TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review the current knowledge about the dynamics of transposable elements at recent evolutionary time scales, and discuss the mechanisms that condition their abundance and frequency. We first discuss non-adaptive mechanisms such as purifying selection and the variable rates of transposition and elimination, and then focus on positive and balancing selection, to finally conclude on the potential role of TEs in causing genomic incompatibilities and eventually speciation. We also suggest possible ways to better model TEs dynamics in a population genomics context by incorporating recent advances in TEs into the rich information provided by SNPs about the demography, selection, and intrinsic properties of genomes.
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Whiteley, A. R., K. N. Persaud, N. Derome, R. Montgomerie, and L. Bernatchez. "Reduced sperm performance in backcross hybrids between species pairs of whitefish (Coregonus clupeaformis)." Canadian Journal of Zoology 87, no. 7 (July 2009): 566–72. http://dx.doi.org/10.1139/z09-042.
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Previous work has demonstrated that genomic incompatibilities work together with ecologically divergent selection to promote and maintain reproductive isolation between incipient species (dwarf and normal) of lake whitefish ( Coregonus clupeaformis (Mitchill, 1818)). Whitefish spawn in groups with external fertilization, which creates conditions for strong sperm competition. In this study, we asked whether reduced sperm performance in hybrids from whitefish species-pair matings might contribute to postzygotic isolating mechanisms between these taxa. We examined two sperm traits, sperm swimming speed and flagellum length, in pure dwarf and normal whitefish and in their F1 and backcross hybrids. We observed significantly reduced sperm swimming speed in backcross but not in F1 hybrids. Sperm flagellum length was not significantly correlated with sperm swimming speed. These results demonstrate that F1 hybrids formed in nature should be capable of the same fertilization success as the parental species during sperm competition, everything else being equal. However, reduced sperm performance in the backcross generation is consistent with other evidence suggesting that genomic incompatibilities create a range of negative fitness effects in post-F1 whitefish hybrids and provides evidence for an additional postzygotic isolation mechanism involved in the incipient speciation of sympatric dwarf and normal whitefish.
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Dufresnes, Christophe, Alan Brelsford, Daniel L. Jeffries, Glib Mazepa, Tomasz Suchan, Daniele Canestrelli, Alfredo Nicieza, et al. "Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation." Proceedings of the National Academy of Sciences 118, no. 36 (August 31, 2021): e2103963118. http://dx.doi.org/10.1073/pnas.2103963118.
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The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.
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Muirhead, Christina A., and Daven C. Presgraves. "Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species." American Naturalist 187, no. 2 (February 2016): 249–61. http://dx.doi.org/10.1086/684583.
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Pulido-Santacruz, Paola, Alexandre Aleixo, and Jason T. Weir. "Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation." Proceedings of the Royal Society B: Biological Sciences 285, no. 1874 (March 7, 2018): 20172081. http://dx.doi.org/10.1098/rspb.2017.2081.
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We possess limited understanding of how speciation unfolds in the most species-rich region of the planet—the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understorey birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understorey forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest old, cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.
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Bailey, Richard I., Fabrice Eroukhmanoff, and Glenn-Peter Sætre. "Hybridization and genome evolution II: Mechanisms of species divergence and their effects on evolution in hybrids." Current Zoology 59, no. 5 (October 1, 2013): 675–85. http://dx.doi.org/10.1093/czoolo/59.5.675.
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Abstract Recent genomic studies have highlighted the importance of hybridization and gene exchange in evolution. We ask what factors cause variation in the impact of hybridization, through adaptation in hybrids and the likelihood of hybrid speciation. During speciation, traits that diverge due to both divergent and stabilizing selection can contribute to the buildup of reproductive isolation. Divergent directional selection in parent taxa should lead to intermediate phenotypes in hybrids, whereas stabilizing selection can also produce extreme, transgressive phenotypes when hybridization occurs. By examining existing theory and empirical data, we discuss how these effects, combined with differences between modes of divergence in the chromosomal distribution of incompatibilities, affect adaptation and speciation in hybrid populations. The result is a clear and testable set of predictions that can be used to examine hybrid adaptation and speciation. Stabilizing selection in parents increases transgression in hybrids, increasing the possibility for novel adaptation. Divergent directional selection causes intermediate hybrid phenotypes and increases their ability to evolve along the direction of parental differentiation. Stabilizing selection biases incompatibilities towards autosomes, leading to reduced sexual correlations in trait values and reduced pleiotropy in hybrids, and hence increased freedom in the direction of evolution. Directional selection causes a bias towards sex-linked incompatibilities, with the opposite consequences. Divergence by directional selection leads to greater dominance effects than stabilizing selection, with major but variable impacts on hybrid evolution.
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Moran, Rachel L., Julian M. Catchen, and Rebecca C. Fuller. "Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation." Molecular Biology and Evolution 37, no. 3 (November 5, 2019): 711–29. http://dx.doi.org/10.1093/molbev/msz260.
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Abstract Comparative genomic approaches are increasingly being used to study the evolution of reproductive barriers in nonmodel species. Although numerous studies have examined prezygotic isolation in darters (Percidae), investigations into postzygotic barriers have remained rare due to long generation times and a lack of genomic resources. Orangethroat and rainbow darters naturally hybridize and provide a remarkable example of male-driven speciation via character displacement. Backcross hybrids suffer from high mortality, which appears to promote behavioral isolation in sympatry. To investigate the genomic architecture of postzygotic isolation, we used Illumina and PacBio sequencing to generate a chromosome-level, annotated assembly of the orangethroat darter genome and high-density linkage maps for orangethroat and rainbow darters. We also analyzed genome-wide RADseq data from wild-caught adults of both species and laboratory-generated backcrosses to identify genomic regions associated with hybrid incompatibles. Several putative chromosomal translocations and inversions were observed between orangethroat and rainbow darters, suggesting structural rearrangements may underlie postzygotic isolation. We also found evidence of selection against recombinant haplotypes and transmission ratio distortion in backcross hybrid genomes, providing further insight into the genomic architecture of genetic incompatibilities. Notably, regions with high levels of genetic divergence between species were enriched for genes associated with developmental and meiotic processes, providing strong candidates for postzygotic isolating barriers. These findings mark significant contributions to our understanding of the genetic basis of reproductive isolation between species undergoing character displacement. Furthermore, the genomic resources presented here will be instrumental for studying speciation in darters, the most diverse vertebrate group in North America.
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Coughlan, Jenn. "One fish, two fish, red fish, dead fish: Detecting the genomic footprint of ecological incompatibilities." PLOS Biology 20, no. 1 (January 11, 2022): e3001504. http://dx.doi.org/10.1371/journal.pbio.3001504.
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Lima, Thiago G., Ronald S. Burton, and Christopher S. Willett. "Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod Tigriopus californicus." Evolution 73, no. 3 (February 8, 2019): 609–20. http://dx.doi.org/10.1111/evo.13690.
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Power, Jeffrey J., Fernanda Pinheiro, Simone Pompei, Viera Kovacova, Melih Yüksel, Isabel Rathmann, Mona Förster, Michael Lässig, and Berenike Maier. "Adaptive evolution of hybrid bacteria by horizontal gene transfer." Proceedings of the National Academy of Sciences 118, no. 10 (March 1, 2021): e2007873118. http://dx.doi.org/10.1073/pnas.2007873118.
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Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.
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Kautt, Andreas F., Claudius F. Kratochwil, Alexander Nater, Gonzalo Machado-Schiaffino, Melisa Olave, Frederico Henning, Julián Torres-Dowdall, et al. "Contrasting signatures of genomic divergence during sympatric speciation." Nature 588, no. 7836 (October 28, 2020): 106–11. http://dx.doi.org/10.1038/s41586-020-2845-0.
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AbstractThe transition from ‘well-marked varieties’ of a single species into ‘well-defined species’—especially in the absence of geographic barriers to gene flow (sympatric speciation)—has puzzled evolutionary biologists ever since Darwin1,2. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories5. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.
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Comeault, Aaron A. "The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation." Ecology and Evolution 8, no. 5 (February 14, 2018): 2926–37. http://dx.doi.org/10.1002/ece3.3872.
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Forsythe, Evan S., Joel Sharbrough, Justin C. Havird, Jessica M. Warren, and Daniel B. Sloan. "CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis." Genome Biology and Evolution 11, no. 8 (July 8, 2019): 2194–202. http://dx.doi.org/10.1093/gbe/evz144.
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AbstractThe function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret, and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.
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Feiner, Nathalie. "Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards." Proceedings of the Royal Society B: Biological Sciences 283, no. 1840 (October 12, 2016): 20161555. http://dx.doi.org/10.1098/rspb.2016.1555.
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Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region ( Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis , TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.
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Chueca, Luis J., Tilman Schell, and Markus Pfenninger. "Whole-genome re-sequencing data to infer historical demography and speciation processes in land snails: the study of two Candidula sister species." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1825 (April 5, 2021): 20200156. http://dx.doi.org/10.1098/rstb.2020.0156.
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Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula . Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
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Vasilopoulou, Christina, Benjamin Wingfield, Andrew P. Morris, and William Duddy. "snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data." F1000Research 10 (November 29, 2021): 567. http://dx.doi.org/10.12688/f1000research.53821.2.
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Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Software incompatibilities, and inconsistencies across computing environments, are recurrent challenges, leading to poor reproducibility. Existing semi-automated or automated solutions lack comprehensive quality checks, flexible workflow architecture, and user control. To address these challenges, we have developed snpQT: a scalable, stand-alone software pipeline using nextflow and BioContainers, for comprehensive, reproducible and interactive quality control of human genomic data. snpQT offers some 36 discrete quality filters or correction steps in a complete standardised pipeline, producing graphical reports to demonstrate the state of data before and after each quality control procedure. This includes human genome build conversion, population stratification against data from the 1,000 Genomes Project, automated population outlier removal, and built-in imputation with its own pre- and post- quality controls. Common input formats are used, and a synthetic dataset and comprehensive online tutorial are provided for testing, educational purposes, and demonstration. The snpQT pipeline is designed to run with minimal user input and coding experience; quality control steps are implemented with numerous user-modifiable thresholds, and workflows can be flexibly combined in custom combinations. snpQT is open source and freely available at https://github.com/nebfield/snpQT. A comprehensive online tutorial and installation guide is provided through to GWAS (https://snpqt.readthedocs.io/en/latest/), introducing snpQT using a synthetic demonstration dataset and a real-world Amyotrophic Lateral Sclerosis SNP-array dataset.
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Ren, Xiujuan, Yuanyi Liu, Yiping Zhao, Bei Li, Dongyi Bai, Gerelchimeg Bou, Xinzhuang Zhang, et al. "Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule." Genes 13, no. 12 (November 23, 2022): 2188. http://dx.doi.org/10.3390/genes13122188.
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Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an Equus parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laboratory. Approximately 24.86 million alleles were discovered that varied from the reference genome. Single nucleotide polymorphisms were used as polymorphic markers for assigning alleles to their parental genomic inheritance. We identified 25,703 Mendelian inheritance error single nucleotide polymorphisms in the mule genome that were not inherited from the parents through Mendelian inheritance. A total of 555 de novo single nucleotide polymorphisms were also identified. The rate of de novo single nucleotide polymorphisms was 2.21 × 10−7 in the mule from the Equus parent-offspring trio. This rate is obviously higher than the natural mutation rate for Equus, which is also consistent with the previous hypothesis that interracial crosses may have a high mutation rate. The genes associated with these single nucleotide polymorphisms are mainly involved in immune processes, DNA repair, and cancer processes. The results of the analysis of three genomes from an Equus parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules.
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Satokangas, I., S. H. Martin, H. Helanterä, J. Saramäki, and J. Kulmuni. "Multi-locus interactions and the build-up of reproductive isolation." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1806 (July 13, 2020): 20190543. http://dx.doi.org/10.1098/rstb.2019.0543.
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All genes interact with other genes, and their additive effects and epistatic interactions affect an organism's phenotype and fitness. Recent theoretical and empirical work has advanced our understanding of the role of multi-locus interactions in speciation. However, relating different models to one another and to empirical observations is challenging. This review focuses on multi-locus interactions that lead to reproductive isolation (RI) through reduced hybrid fitness. We first review theoretical approaches and show how recent work incorporating a mechanistic understanding of multi-locus interactions recapitulates earlier models, but also makes novel predictions concerning the build-up of RI. These include high variance in the build-up rate of RI among taxa, the emergence of strong incompatibilities producing localized barriers to introgression, and an effect of population size on the build-up of RI. We then review recent experimental approaches to detect multi-locus interactions underlying RI using genomic data. We argue that future studies would benefit from overlapping methods like ancestry disequilibrium scans, genome scans of differentiation and analyses of hybrid gene expression. Finally, we highlight a need for further overlap between theoretical and empirical work, and approaches that predict what kind of patterns multi-locus interactions resulting in incompatibilities will leave in genome-wide polymorphism data. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.
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Stalker, H. T., S. P. Tallury, P. Ozias-Akins, D. Bertioli, and S. C. Leal Bertioli. "The Value of Diploid Peanut Relatives for Breeding and Genomics." Peanut Science 40, no. 2 (July 1, 2013): 70–88. http://dx.doi.org/10.3146/ps13-6.1.
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ABSTRACT Collection, evaluation, and introgression research has been conducted with Arachis species for more than 60 years. Eighty species in the genus have been described and additional species will be named in the future. Extremely high levels of disease and insect resistances to immunity have been observed in many species of the genus as compared to the cultivated peanut, which makes them extremely important for crop improvement. Many thousands of interspecific hybrids have been produced in the genus, but introgression has been slow because of genomic incompatibilities and sterility of hybrids. Genomics research was initiated during the late 1980s to characterize species relationships and investigate more efficient methods to introgress genes from wild species to A. hypogaea. Relatively low density genetic maps have been created from inter- and intra-specific crosses, several of which have placed disease resistance genes into limited linkage groups. Of particular interest is associating molecular markers with traits of interest to enhance breeding for disease and insect resistances. Only recently have sufficiently large numbers of markers become available to effectively conduct marker assisted breeding in peanut. Future analyses of the diploid ancestors of the cultivated peanut, A. duranensis and A. ipaensis, will allow more detailed characterization of peanut genetics and the effects of Arachis species alleles on agronomic traits. Extensive efforts are being made to create populations for genomic analyses of peanut, and introgression of genes from wild to cultivated genotypes should become more efficient in the near future.
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Senerchia, Natacha, François Felber, and Christian Parisod. "Genome reorganization in F 1 hybrids uncovers the role of retrotransposons in reproductive isolation." Proceedings of the Royal Society B: Biological Sciences 282, no. 1804 (April 7, 2015): 20142874. http://dx.doi.org/10.1098/rspb.2014.2874.
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Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F 1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F 1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F 1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation.
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Kuhlman, Les C., Byron L. Burson, Patricia E. Klein, Robert R. Klein, David M. Stelly, H. James Price, and William L. Rooney. "Genetic recombination in Sorghum bicolor × S. macrospermum interspecific hybrids." Genome 51, no. 9 (September 2008): 749–56. http://dx.doi.org/10.1139/g08-061.
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Sorghum has been improved by public and private breeding programs utilizing germplasm mostly from within the species Sorghum bicolor . Until recently, cross-incompatibilities have prevented hybridization of S. bicolor with most other species within the genus Sorghum . Utilizing germplasm homozygous for the iap allele, hybrids were readily produced between S. bicolor (2n = 20; AAB1B1) and S. macrospermum (2n = 40; WWXXYYZZ). These hybrids were intermediate to the parents in chromosome number (2n = 30) and overall morphology. Meiosis in both parents was regular; S. bicolor had 10 bivalents per pollen mother cell (PMC) and S. macrospermum had an average of 19.96 bivalents per PMC. Six hybrids were studied cytologically and meiosis was irregular, with the chromosomes associating primarily as univalents and bivalents. There was an average of 3.54 bivalents per PMC, with a range of 0–8 bivalents, most of which were rods (98%). Using FISH (fluorescent in situ hybridization), moderate levels (2.6 II per PMC) of allosyndetic recombination were observed. Genomic relationships were sufficient to assign S. macrospermum the genomic formula AAB1B1YYZZ (Y and Z remain unknown). Allosyndetic recombination in the interspecific hybrids indicates that introgression through genetic recombination should be possible if viable backcrosses can be recovered.
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Morales, Lucia, and Bernard Dujon. "Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts." Microbiology and Molecular Biology Reviews 76, no. 4 (November 29, 2012): 721–39. http://dx.doi.org/10.1128/mmbr.00022-12.
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SUMMARYForced interspecific hybridization has been used in yeasts for many years to study speciation or to construct artificial strains with novel fermentative and metabolic properties. Recent genome analyses indicate that natural hybrids are also generated spontaneously between yeasts belonging to distinct species, creating lineages with novel phenotypes, varied genetic stability, or altered virulence in the case of pathogens. Large segmental introgressions from evolutionarily distant species are also visible in some yeast genomes, suggesting that interspecific genetic exchanges occur during evolution. The origin of this phenomenon remains unclear, but it is likely based on weak prezygotic barriers, limited Dobzhansky-Muller (DM) incompatibilities, and rapid clonal expansions. Newly formed interspecies hybrids suffer rapid changes in the genetic contribution of each parent, including chromosome loss or aneuploidy, translocations, and loss of heterozygosity, that, except in a few recently studied cases, remain to be characterized more precisely at the genomic level by use of modern technologies. We review here known cases of natural or artificially formed interspecies hybrids between yeasts and discuss their potential importance in terms of genome evolution. Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes.
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Dufresnes, Christophe, and Íñigo Martínez-Solano. "Hybrid zone genomics supports candidate species in Iberian Alytes obstetricans." Amphibia-Reptilia 41, no. 1 (June 12, 2020): 105–12. http://dx.doi.org/10.1163/15685381-20191312.
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Abstract While estimates of genetic divergence are increasingly used in molecular taxonomy, hybrid zone analyses can provide decisive evidence for evaluating candidate species. Applying a population genomic approach (RAD-sequencing) to a fine-scale transect sampling, we analyzed the transition between two Iberian subspecies of the common midwife toad (Alytes obstetricans almogavarii and A. o. pertinax) in Catalonia (northeastern Spain), which putatively diverged since the Plio-Pleistocene. Their hybrid zone was remarkably narrow, with extensive admixture restricted to a single locality (close to Tarragona), and congruent allele frequency clines for the mitochondrial (13 km wide) and the average nuclear genomes (16 km wide). We also fitted clines independently for 89 taxon-diagnostic SNPs: most of them behave like the nuclear background, but a subset (13%) is completely impermeable to gene flow and might be linked to barrier loci involved in hybrid incompatibilities. Assuming that midwife toads are able to disperse in the area of contact, we conclude that these taxa experience partial reproductive isolation and represent incipient species, i.e. Alytes almogavarii and Alytes obstetricans. Interestingly, their evolutionary age and mitochondrial divergence fall below the thresholds proposed in molecular systematics studies, emphasizing the difficulty of predicting the outcome of secondary contacts between young lineages entering the grey zone of speciation.
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Xie, Hai-Bing, Li-Gang Wang, Chen-Yu Fan, Long-Chao Zhang, Adeniyi C. Adeola, Xue Yin, Zhao-Bang Zeng, Li-Xian Wang, and Ya-Ping Zhang. "Genetic Architecture Underlying Nascent Speciation—The Evolution of Eurasian Pigs under Domestication." Molecular Biology and Evolution 38, no. 9 (April 21, 2021): 3556–66. http://dx.doi.org/10.1093/molbev/msab117.
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Abstract Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in the advanced stages of speciation, the genetics of reproductive isolation in nascent stage of speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying the early stages of speciation in great details. Pig breeds have not evolved the large X-effect of hybrid incompatibility commonly observed between “good species.” Instead, deleterious epistatic interactions among multiple autosomal loci are common. These weak Dobzhansky–Muller incompatibilities confer partial hybrid inviability with sex biases in crosses between European and East Asian domestic pigs. The genomic incompatibility is enriched in pathways for angiogenesis, androgen receptor signaling and immunity, with an observation of many highly differentiated cis-regulatory variants. Our study suggests that partial hybrid inviability caused by pervasive but weak interactions among autosomal loci may be a hallmark of nascent speciation in mammals.
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Demogines, Ann, Alex Wong, Charles Aquadro, and Eric Alani. "Incompatibilities Involving Yeast Mismatch Repair Genes: A Role for Genetic Modifiers and Implications for Disease Penetrance and Variation in Genomic Mutation Rates." PLoS Genetics 4, no. 6 (June 20, 2008): e1000103. http://dx.doi.org/10.1371/journal.pgen.1000103.
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Fel-Clair, Fabienne, Thomas Lenormand, Josette Catalan, Jacqueline Grobert, Annie Orth, Pierre Boursot, Marie-Cecile Viroux, and Janice Britton-Davidian. "Genomic incompatibilities in the hybrid zone between house mice in Denmark: evidence from steep and non-coincident chromosomal clines for Robertsonian fusions." Genetical Research 67, no. 2 (April 1996): 123–34. http://dx.doi.org/10.1017/s0016672300033589.
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SummaryThe pattern of chromosomal variation is investigated in house mice from the Danish hybrid zone between the translocation-prone Mus musculus domesticus and the chromosomally conservative M. m. musculus. The cytogenetic analysis confirmed the non-introgression of three pairs of Robertsonian (Rb) fusions from M. m. domesticus into the M. m. musculus genome. The geographic distribution of two of these Rb fusions was shown to follow staggered chromosomal clines which increased in steepness the closer they were to the centre of the hybrid zone as defined by allozymes. Analysis of alternate hypotheses suggests that chromosomal differentiation of the Danish domesticus occurred after contact was established with musculus. The staggering of the clines would reflect the order of arrival of theRb fusions into the hybrid zone. Several models with different processes of underdominance of the chromosomal heterozygotes are discussed to account for the difference in width between clines. A selective model with increasing levels of genomic underdominance due to interaction with a progressively enriched musculus genome provides the best fit for the observed pattern. Selection against Rb fusions with little effect on the recombination of linked allozyme markers supportsthe view that no reduction in gene flow due to chromosomal heterozygosity is yet apparent through the hybrid zone and that only the centromeric segments of the Rb fusions are incompatible with the musculus genome.
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Rowe, Melissah, Emma Whittington, Kirill Borziak, Mark Ravinet, Fabrice Eroukhmanoff, Glenn-Peter Sætre, and Steve Dorus. "Molecular Diversification of the Seminal Fluid Proteome in a Recently Diverged Passerine Species Pair." Molecular Biology and Evolution 37, no. 2 (October 30, 2019): 488–506. http://dx.doi.org/10.1093/molbev/msz235.
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Abstract Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recently diverged passerine species pair (Passer domesticus and Passer hispaniolensis) using a combination of proteomic and comparative evolutionary genomic approaches. First, we characterized and compared the SF proteome of the two species, revealing consistencies with known aspects of SFP biology and function in other taxa, including the presence and diversification of proteins involved in immunity and sperm maturation. Second, using whole-genome resequencing data, we assessed patterns of genomic differentiation between house and Spanish sparrows. These analyses detected divergent selection on immunity-related SF genes and positive selective sweeps in regions containing a number of SF genes that also exhibited protein abundance diversification between species. Finally, we analyzed the molecular evolution of SFPs across 11 passerine species and found a significantly higher rate of positive selection in SFPs compared with the rest of the genome, as well as significant enrichments for functional pathways related to immunity in the set of positively selected SF genes. Our results suggest that selection on immunity pathways is an important determinant of passerine SF composition and evolution. Assessing the role of immunity genes in speciation in other recently diverged taxa should be prioritized given the potential role for immunity-related proteins in reproductive incompatibilities in Passer sparrows.
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Kazi, A. Mujeeb, Niaz Ali, Amir Ibrahim, Abdul Aziz Napar, M. Jamil, Sajjad Hussain, Zahid Mahmood, et al. "Tissue Culture Mediated Allelic Diversification and Genomic Enrichment of Wheat to Combat Production Constraints and Address Food Security." Plant Tissue Culture and Biotechnology 27, no. 1 (December 27, 2017): 89–140. http://dx.doi.org/10.3329/ptcb.v27i1.35018.
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In view of the emerging population trends and that wheat crop is the major unequivocally recognized conduit towards addressing the food security challenges of 2050 this discourse embraces various research options that are viewed as possible solutions toward delivering those targets for providing nutritious food and meeting the aspirations that policy setters have debated on the subject for decades. The underlying strength for achieving these targets will require concerted efforts from plant researchers that are well integrated within effectively harnessing and utilizing prevalent genetic diversity of the wide array of alleles in a holistic pro‐active manner. We argue that the purists of basic and strategic research dimensions need to be thoughtfully defined, so that the vital target of delivering the “applied” gains are only realized from the outputs on farmer’s fields and measured by tons per hectare. In this quest, the pre‐breeding disciplines “classical mode” and its recently surfaced “modified sense” are pivotal, where within the former facet “tissue culture” (TC)/artificial culturing is embodied integrally. Taken for granted, TC has been the backbone of all wide hybridization studies and has made an enormous impact on the agricultural landscape spanning over the last six decades. With its intervention significant generic and specific incompatibilities have been overcome as well as allowing researchers to exploit the protocols for adding efficiency to breeding programs, facilitate operational technologies in running breeding programs and development of unique genetic stocks that preserve valuable allelic richness in user friendly forms for future free germplasmusage in global/private domains of plant improvement ventures.Plant Tissue Cult. & Biotech. 27(1): 89-140, 2017 (June)
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Han, Ziduan, Wen-Sui Lo, James W. Lightfoot, Hanh Witte, Shuai Sun, and Ralf J. Sommer. "Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes." Genetics 216, no. 4 (October 15, 2020): 947–56. http://dx.doi.org/10.1534/genetics.120.303785.
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A lack of appropriate molecular tools is one obstacle that prevents in-depth mechanistic studies in many organisms. Transgenesis, clustered regularly interspaced short palindromic repeats (CRISPR)-associated engineering, and related tools are fundamental in the modern life sciences, but their applications are still limited to a few model organisms. In the phylum Nematoda, transgenesis can only be performed in a handful of species other than Caenorhabditis elegans, and additionally, other species suffer from significantly lower transgenesis efficiencies. We hypothesized that this may in part be due to incompatibilities of transgenes in the recipient organisms. Therefore, we investigated the genomic features of 10 nematode species from three of the major clades representing all different lifestyles. We found that these species show drastically different codon usage bias and intron composition. With these findings, we used the species Pristionchus pacificus as a proof of concept for codon optimization and native intron addition. Indeed, we were able to significantly improve transgenesis efficiency, a principle that may be usable in other nematode species. In addition, with the improved transgenes, we developed a fluorescent co-injection marker in P. pacificus for the detection of CRISPR-edited individuals, which helps considerably to reduce associated time and costs.
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Yi, MinKyung, Yinghong Ma, Jeremy Yates, and Stanley M. Lemon. "Compensatory Mutations in E1, p7, NS2, and NS3 Enhance Yields of Cell Culture-Infectious Intergenotypic Chimeric Hepatitis C Virus." Journal of Virology 81, no. 2 (November 1, 2006): 629–38. http://dx.doi.org/10.1128/jvi.01890-06.
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ABSTRACT There is little understanding of mechanisms underlying the assembly and release of infectious hepatitis C virus (HCV) from cultured cells. Cells transfected with synthetic genomic RNA from a unique genotype 2a virus (JFH1) produce high titers of virus, while virus yields are much lower with a prototype genotype 1a RNA containing multiple cell culture-adaptive mutations (H77S). To characterize the basis for this difference in infectious particle production, we constructed chimeric genomes encoding the structural proteins of H77S within the background of JFH1. RNAs encoding polyproteins fused at the NS2/NS3 junction (“H-NS2/NS3-J”) and at a site of natural, intergenotypic recombination within NS2 [“H-(NS2)-J”] produced infectious virus. In contrast, no virus was produced by a chimera fused at the p7-NS2 junction. Chimera H-NS2/NS3-J virus (vH-NS2/NS3-J) recovered from transfected cultures contained compensatory mutations in E1 and NS3 that were essential for the production of infectious virus, while yields of infectious vH-(NS2)-J were enhanced by mutations within p7 and NS2. These compensatory mutations were chimera specific and did not enhance viral RNA replication or polyprotein processing; thus, they likely compensate for incompatibilities between proteins of different genotypes at sites of interactions essential for virus assembly and/or release. Mutations in p7 and NS2 acted additively and increased the specific infectivity of vH-(NS2)-J particles, while having less impact on the numbers of particles released. We conclude that interactions between NS2 and E1 and p7 as well as between NS2 and NS3 are essential for virus assembly and/or release and that each of these viral proteins plays an important role in this process.
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Thierry, Maud, Florian Charriat, Joëlle Milazzo, Henri Adreit, Sébastien Ravel, Sandrine Cros-Arteil, Sonia borron, et al. "Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities." PLOS Pathogens 18, no. 7 (July 25, 2022): e1010687. http://dx.doi.org/10.1371/journal.ppat.1010687.
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Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
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Glunčić, Matko, Ines Vlahović, Leo Mršić, and Vladimir Paar. "Global Repeat Map (GRM) Application: Finding All DNA Tandem Repeat Units." Algorithms 15, no. 12 (December 5, 2022): 458. http://dx.doi.org/10.3390/a15120458.
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Tandem repeats (TRs) are important components of eukaryotic genomes; they have both structural and functional roles: (i) they form essential chromosome structures such as centromeres and telomeres; (ii) they modify chromatin structure and affect transcription, resulting in altered gene expression and protein abundance. There are established links between variations in TRs and incompatibilities between species, evolutionary development, chromosome mis-segregation, aging, cancer outcomes and different diseases. Given the importance of TRs, it seemed essential to develop an efficient, sensitive and automated application for the identification of all kinds of TRs in various genomic sequences. Here, we present our new GRM application for identifying TRs, which is designed to overcome all the limitations of the currently existing algorithms. Our GRM algorithm provides a straightforward identification of TRs using the frequency domain but avoiding the mapping of the symbolic DNA sequence into numerical sequence, and using key string matching, but avoiding the statistical methods of locally optimizing individual key strings. Using the GRM application, we analyzed human, chimpanzee and mouse chromosome 19 genome sequences (RefSeqs), and showed that our application was very fast, efficient and simple, with a powerful graphical user interface. It can identify all types of TRs, from the smallest (2 bp) to the very large, as large as tens of kilobasepairs. It does not require any prior knowledge of sequence structure and does not require any user-defined parameters or thresholds. In this way, it ensures that a full spectrum of TRs can be detected in just one step. Furthermore, it is robust to all types of mutations in repeat copies and can identify TRs with various complexities in the sequence pattern. From this perspective, we can conclude that the GRM application is an efficient, sensitive and automated method for the identification of all kinds of TRs.
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Liénard, Marjorie A., Luciana O. Araripe, and Daniel L. Hartl. "Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids." Proceedings of the National Academy of Sciences 113, no. 29 (June 29, 2016): E4200—E4207. http://dx.doi.org/10.1073/pnas.1608337113.
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Crosses between closely related animal species often result in male hybrids that are sterile, and the molecular and functional basis of genetic factors for hybrid male sterility is of great interest. Here, we report a molecular and functional analysis of HMS1, a region of 9.2 kb in chromosome 3 of Drosophila mauritiana, which results in virtually complete hybrid male sterility when homozygous in the genetic background of sibling species Drosophila simulans. The HMS1 region contains two strong candidate genes for the genetic incompatibility, agt and Taf1. Both encode unrelated DNA-binding proteins, agt for an alkyl-cysteine-S-alkyltransferase and Taf1 for a subunit of transcription factor TFIID that serves as a multifunctional transcriptional regulator. The contribution of each gene to hybrid male sterility was assessed by means of germ-line transformation, with constructs containing complete agt and Taf1 genomic sequences as well as various chimeric constructs. Both agt and Taf1 contribute about equally to HMS1 hybrid male sterility. Transgenes containing either locus rescue sterility in about one-half of the males, and among fertile males the number of offspring is in the normal range. This finding suggests compensatory proliferation of the rescued, nondysfunctional germ cells. Results with chimeric transgenes imply that the hybrid incompatibilities result from interactions among nucleotide differences residing along both agt and Taf1. Our results challenge a number of preliminary generalizations about the molecular and functional basis of hybrid male sterility, and strongly reinforce the role of DNA-binding proteins as a class of genes contributing to the maintenance of postzygotic reproductive isolation.
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Sansinena, Marina J., John Lynn, Kenneth R. Bondioli, Richard S. Denniston, and Robert A. Godke. "Ooplasm transfer and interspecies somatic cell nuclear transfer: heteroplasmy, pattern of mitochondrial migration and effect on embryo development." Zygote 19, no. 2 (August 25, 2010): 147–56. http://dx.doi.org/10.1017/s0967199410000419.
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SummaryAlthough interspecies somatic cell nuclear transfer (iSCNT) has potential applications in the conservation of exotic species, an in vitro developmental block has been observed in embryos produced by this approach. It has been suggested that mitochondrial mismatch between donor cell and recipient oocyte could cause embryonic developmental arrest. A series of experiments was conducted to investigate the effect of mixed mitochondrial populations (heteroplasmy) on early development of iSCNT-derived cloned embryos. The effect of combining the techniques of ooplasm transfer (OT) and somatic cell nuclear transfer (SCNT) was examined by monitoring in vitro embryonic development; the presence and pattern of migration of foreign mitochondria after OT was analysed by MitoTracker staining. In addition, the effect of transferring caprine ooplasm (iOT) into the bovine enucleated oocytes used in iSCNT was analysed. There was no significant effect of the sequence of events (OT-SCNT or SCNT-OT) on the number of fused, cleaved, blastocyst or hatched blastocyst stage embryos. MitoTracker Green staining of donor oocytes used for OT confirmed the introduction of foreign mitochondria. The distribution pattern of transferred mitochondria most commonly remained in a distinct cluster after 12, 74 and 144 h of in vitro culture. When goat ooplasm was injected into bovine enucleated oocytes (iSCNT), there was a reduction (p < 0.05) in fusion (52 vs. 82%) and subsequent cleavage rates (55 vs. 78%). The procedure of iOT prior to iSCNT had no effect in overcoming the 8- to 16-cell in vitro developmental block, and only parthenogenetic cow and goat controls reached the blastocyst (36 and 32%) and hatched blastocyst (25 and 12%) stages, respectively. This study indicates that when foreign mitochondria are introduced at the time of OT, these organelles tend to remain as distinct clusters without relocation after a few mitotic divisions. Although the bovine cytoplast appears capable of supporting mitotic divisions after iOT-iSCNT, heteroplasmy or mitochondrial incompatibilities may affect nuclear-ooplasmic events occurring at the time of genomic activation.
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Postel, Zoé, and Pascal Touzet. "Cytonuclear Genetic Incompatibilities in Plant Speciation." Plants 9, no. 4 (April 10, 2020): 487. http://dx.doi.org/10.3390/plants9040487.
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Due to the endosymbiotic origin of organelles, a pattern of coevolution and coadaptation between organellar and nuclear genomes is required for proper cell function. In this review, we focus on the impact of cytonuclear interaction on the reproductive isolation of plant species. We give examples of cases where species exhibit barriers to reproduction which involve plastid-nuclear or mito-nuclear genetic incompatibilities, and describe the evolutionary processes at play. We also discuss potential mechanisms of hybrid fitness recovery such as paternal leakage. Finally, we point out the possible interplay between plant mating systems and cytonuclear coevolution, and its consequence on plant speciation.
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Walter, Stephanie, Alexander Bollenbach, Juliane Doerrbecker, Stephanie Pfaender, Richard J. P. Brown, Gabrielle Vieyres, Claire Scott, et al. "Ion Channel Function and Cross-Species Determinants in Viral Assembly of Nonprimate Hepacivirus p7." Journal of Virology 90, no. 10 (March 9, 2016): 5075–89. http://dx.doi.org/10.1128/jvi.00132-16.
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ABSTRACTNonprimate hepacivirus (NPHV), the closest homolog of hepatitis C virus (HCV) described to date, has recently been discovered in horses. Even though the two viruses share a similar genomic organization, conservation of the encoded hepaciviral proteins remains undetermined. The HCV p7 protein is localized within endoplasmic reticulum (ER) membranes and is important for the production of infectious particles. In this study, we analyzed the structural and functional features of NPHV p7 in addition to its role during virus assembly. Three-dimensional homology models for NPHV p7 using various nuclear magnetic resonance spectroscopy (NMR) structures were generated, highlighting the conserved residues important for ion channel function. By applying a liposome permeability assay, we observed that NPHV p7 exhibited liposome permeability features similar to those of HCV p7, indicative of similar ion channel activity. Next, we characterized the viral protein using a p7-basedtrans-complementation approach. A similar subcellular localization pattern at the ER membrane was observed, although production of infectious particles was likely hindered by genetic incompatibilities with HCV proteins. To further characterize these cross-species constraints, chimeric viruses were constructed by substituting different regions of HCV p7 with NPHV p7. The N terminus and transmembrane domains were nonexchangeable and therefore constitute a cross-species barrier in hepaciviral assembly. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectioustrans-complemented viral particles. In conclusion, comparison of NPHV and HCV p7 revealed structural and functional homology of these proteins, including liposome permeability, and broadly acting determinants that modulate hepaciviral virion assembly and contribute to the host-species barrier were identified.IMPORTANCEThe recent discovery of new relatives of hepatitis C virus (HCV) enables for the first time the study of cross-species determinants shaping hepaciviral pathogenesis. Nonprimate hepacivirus (NPHV) was described to infect horses and represents so far the closest homolog of HCV. Both viruses encode the same viral proteins; however, NPHV protein functions remain poorly understood. In this study, we aimed to dissect NPHV p7 on a structural and functional level. By using various NMR structures of HCV p7 as templates, three-dimensional homology models for NPHV p7 were generated, highlighting conserved residues that are important for ion channel function. A p7-basedtrans-complementation approach and the construction of NPHV/HCV p7 chimeric viruses showed that the N terminus and transmembrane domains were nonexchangeable. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectious viral particles. These results identify species-specific constraints as well as exchangeable determinants in hepaciviral assembly.
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Presgraves, Daven C. "A Fine-Scale Genetic Analysis of Hybrid Incompatibilities in Drosophila." Genetics 163, no. 3 (March 1, 2003): 955–72. http://dx.doi.org/10.1093/genetics/163.3.955.
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Abstract The sterility and inviability of species hybrids is thought to evolve by the accumulation of genes that cause generally recessive, incompatible epistatic interactions between species. Most analyses of the loci involved in such hybrid incompatibilities have suffered from low genetic resolution. Here I present a fine-resolution genetic screen that allows systematic counting, mapping, and characterizing of a large number of hybrid incompatibility loci in a model genetic system. Using small autosomal deletions from D. melanogaster and a hybrid rescue mutation from D. simulans, I measured the viability of hybrid males that are simultaneously hemizygous for a small region of the D. simulans autosomal genome and hemizygous for the D. melanogaster X chromosome. These hybrid males are exposed to the full effects of any recessive-recessive epistatic incompatibilities present in these regions. A screen of ∼70% of the D. simulans autosomal genome reveals 20 hybrid-lethal and 20 hybrid-semilethal regions that are incompatible with the D. melanogaster X. In further crosses, I confirm the epistatic nature of hybrid lethality by showing that all of the incompatibilities are rescued when the D. melanogaster X is replaced with a D. simulans X. Combined with information from previous studies, these results show that the number of recessive incompatibilities is approximately eightfold larger than the number of dominant ones. Finally, I estimate that a total of ∼191 hybrid-lethal incompatibilities separate D. melanogaster and D. simulans, indicating extensive functional divergence between these species’ genomes.
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Colomé-Tatché, Maria, and Frank Johannes. "Signatures of Dobzhansky–Muller Incompatibilities in the Genomes of Recombinant Inbred Lines." Genetics 202, no. 2 (December 17, 2015): 825–41. http://dx.doi.org/10.1534/genetics.115.179473.
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Tobler, M., N. Barts, and R. Greenway. "Mitochondria and the Origin of Species: Bridging Genetic and Ecological Perspectives on Speciation Processes." Integrative and Comparative Biology 59, no. 4 (April 20, 2019): 900–911. http://dx.doi.org/10.1093/icb/icz025.
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Abstract Mitochondria have been known to be involved in speciation through the generation of Dobzhansky–Muller incompatibilities, where functionally neutral co-evolution between mitochondrial and nuclear genomes can cause dysfunction when alleles are recombined in hybrids. We propose that adaptive mitochondrial divergence between populations can not only produce intrinsic (Dobzhansky–Muller) incompatibilities, but could also contribute to reproductive isolation through natural and sexual selection against migrants, post-mating prezygotic isolation, as well as by causing extrinsic reductions in hybrid fitness. We describe how these reproductive isolating barriers can potentially arise through adaptive divergence of mitochondrial function in the absence of mito-nuclear coevolution, a departure from more established views. While a role for mitochondria in the speciation process appears promising, we also highlight critical gaps of knowledge: (1) many systems with a potential for mitochondrially-mediated reproductive isolation lack crucial evidence directly linking reproductive isolation and mitochondrial function; (2) it often remains to be seen if mitochondrial barriers are a driver or a consequence of reproductive isolation; (3) the presence of substantial gene flow in the presence of mito-nuclear incompatibilities raises questions whether such incompatibilities are strong enough to drive speciation to completion; and (4) it remains to be tested how mitochondrial effects on reproductive isolation compare when multiple mechanisms of reproductive isolation coincide. We hope this perspective and the proposed research plans help to inform future studies of mitochondrial adaptation in a manner that links genotypic changes to phenotypic adaptations, fitness, and reproductive isolation in natural systems, helping to clarify the importance of mitochondria in the formation and maintenance of biological diversity.
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Sansinena, M., J. Lynn, R. Denniston, and R. Godke. "64 OOPLASMIC TRANSFER AFTER INTERSPECIES NUCLEAR TRANSFER: PRESENCE OF FOREIGN MITOCHONDRIA, PATTERN OF MIGRATION, AND EFFECT ON EMBRYO DEVELOPMENT." Reproduction, Fertility and Development 17, no. 2 (2005): 182. http://dx.doi.org/10.1071/rdv17n2ab64.
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Interspecies somatic cell nuclear transfer (iSCNT) using the bovine cytoplast as universal recipient has potential applications in the conservation of exotic species. However, an in vitro developmental block has been observed using this approach. It has been suggested that mitochondrial mismatch between donor cell and recipient oocyte could be a cause for the embryonic developmental arrest. A series of experiments were conducted to investigate the effect of mixed mitochondrial populations (heteroplasmy) on early development of cloned embryos. In Experiment 1, we examined the effect of combining the technique of ooplasmic transfer (OT) with somatic cell nuclear transfer (SCNT) in the bovine model. In addition, presence and pattern of migration of foreign mitochondria after OT were examined by MitoTracker® (Molecular Probes, Inc., Eugene, OR, USA) staining. In Experiment 2, we examined the effect of transferring caprine ooplasm into bovine enucleated oocytes (iOT) used as recipients for goat iSCNT. Ooplasm from donor oocytes was aspirated until the oolema was ruptured and filled about 200 μm of the micropipette. Aspirated ooplasm was injected into recipient oocyte; the oolema of the recipient oocyte was also ruptured by partial aspiration into the micropipette to ensure mixing. Mean cleavage rates and embryo development were compared by chi-square analysis. Percentages (except for parthenogenic controls) were calculated from number of fused couplets. In Experiment 1, there was no significant effect of the sequence of events (OT-SCNT or SCNT-OT) on the number of fused, cleaved, blastocyst (BLST), or hatched blastocyst (HCHD) embryos (Table 1). MitoTracker Green FM staining of donor oocytes used for OT revealed foreign mitochondria were introduced by the procedure. Their pattern of distribution remained in a distinct cluster after 12, 74 and 144 h of in vitro culture. However, when goat ooplasm was injected into bovine enucleated oocytes used for iSCNT, there was a significant reduction in fusion (52 vs. 82%) and cleavage rates (55 vs. 78%) (P < 0.05). In addition, the procedure of iOT prior to iSCNT was not effective in overcoming the 8- to 16-cell in vitro developmental block and only parthenogenic cow and goat controls reached blastocyst (36 and 32%) and hatched blastocyst (25 and 12%) stages, respectively (Table 1). This study demonstrates that foreign mitochondria are introduced at the time of OT and these mitochondria remain in a cluster without relocation after a few mitotic divisions. Although the bovine cytoplast appears capable of supporting mitotic divisions after iOT-iSCNT, heteroplasmy or mitochondrial incompatibilities may affect nuclear-ooplasmic events occurring at genomic activation. To our knowledge, this is the first scientific report of iOT used in combination with iSCNT in an attempt to overcome the in vitro developmental block. Further research is needed to determine characteristics of foreign mitochondrial dynamics as well as replication of foreign mitochondria introduced into NT embryos. Table 1. Intraspecies (cow) and interspecies (goat-cow) ooplasmic transfer and nuclear transfer
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Gómez, M. C., J. I. Lyons, C. E. Pope, M. Biancardi, C. Dumas, J. Galiguis, G. Wang, and B. L. Dresser. "56 EFFECTS OF PHYLOGENIC GENERA OF RECIPIENT CYTOPLASTS ON DEVELOPMENT AND VIABILITY OF CANADA LYNX (LYNX CANADENSIS) CLONED EMBRYOS." Reproduction, Fertility and Development 22, no. 1 (2010): 186. http://dx.doi.org/10.1071/rdv22n1ab56.
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Canada lynx (Lynx canadensis; CL) once occupied 16 states in the Unites States of America, but small populations remain in only 3 states. Interspecies-somatic cell nuclear transfer (Is-SCNT) offers the possibility of preventing their extinction; however, developmental constraints on Is-SCNT embryos are proportional to the phylogenetic distance between the donor cell and the recipient oocyte. Mitochondrial DNA (mtDNA) heteroplasmy may be involved in nuclear-cytoplasmic incompatibilities, thus inhibiting development of cloned embryos at the time of genomic activation. Minimizing the phylogenetic distance between the donor cell and recipient oocyte may enhance development of clone embryos. Caracal (Caracal caracal) may be suitable as an oocyte donor for SCNT and a recipient of CL cloned embryos because caracals hybridize with other felid species and share physical characteristics with the lynx family, marked by being previously classified in the lynx genera and having similar gestational length. To ensure compatibilities between the donor nuclei of the CL and the mitochondria of recipient oocytes, we (1) compared in vitro development of CL cloned embryos reconstructed with domestic cat (Felis catus; DSH) or caracal cytoplasts, (2) examined the mtDNA genotypes in CL cloned embryos, and (3) evaluated in vivo developmental competence of CL cloned embryos after transfer into caracal recipients. A total of 160 and 217 preovulatory oocytes were collected by laparoscopy from gonadotropin-treated caracals (n = 8) and DSH (n = 10) and used as recipient cytoplasts for reconstructing CL embryos. Results indicated that the phylogenetic genera of recipient cytoplasts did not affect embryo cleavage at Day 2 (caracal 50/55, 91% v. DSH 63/65, 97%), but development of CL cloned embryos to the blastocyst stage was higher when caracal oocytes were used as recipient cytoplasts (15/50; 30%) than with DSH cytoplasts (9/63, 14%; P < 0.05). The extent of mtDNA homoplasmy or heteroplasmy in CL cloned embryos was calculated by the number of single nucleotide polymorphisms (SNP) derived from the DSH or caracal oocyte donors and from the somatic cell donor CL. DNA was isolated from 25 and 35 CL cloned embryos reconstructed with caracal or DSH cytoplasts, respectively. All amplified products after PCR were sequenced and SNP analyzed. All CL embryos reconstructed with DSH cytoplasts were homoplasmic, carrying mtDNA only from the DSH oocyte donor (n = 35; SNP DSH = 2-6). Embryos reconstructed with caracal cytoplasts were homoplasmic for CL mtDNA (n = 9; SNPCL = 10-12) or heteroplasmic (caracal × CL, n = 17; SNPCL = 7-9; SNP caracal = 2-3). A total of 69 (mean = 34.5 ± 4.9 per caracal) and 70 (mean = 35.0 ± 9.8 per caracal) CL cloned embryos reconstructed with caracal and DSH cytoplasts, respectively, were transferred into 4 caracal recipients; however, no pregnancies were established. In summary, Is-SCNT between 2 phylogenetically closer species favors retention of the donor’s mitochondria, which might lead to a better nucleo-cytoplasmic interaction for reprogramming of donor nucleus.
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Hill, Geoffrey E. "Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression." Integrative and Comparative Biology 59, no. 4 (April 27, 2019): 912–24. http://dx.doi.org/10.1093/icb/icz019.
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Abstract The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.