Additive and non-additive epigenetic signatures of hybridisation between fish species with different mating systems

AbstractHybridisation is a major source of evolutionary innovation. However, several prezygotic and postzygotic factors influence its likelihood and evolutionary outcomes. Differences in mating systems can have a major effect on the extent and direction of hybridisation and introgression. In plants, epigenetic mechanisms help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the extent of a unique case of natural hybridisation between two genetically distant mangrove killifish species with different mating systems, Kryptolebias hermaphroditus (self-fertilising) and K. ocellatus (outcrossing), and the methylation patterns of their hybrids. Hybridisation rate between the species ranged between 14% and 26%. Although co-existing parental species displayed highly distinct genetic (microsatellites and SNPs) and methylation patterns (37,000 differentially methylated cytosines), our results indicate that F1 hybrids are viable and able to backcross with parental species. Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridisation between genetically distant species. Differentially methylated cytosines between hybrids and both parental species (5,800) suggest that introgressive hybridisation may play a role in generating novel genetic and epigenetic variation which could lead to species diversification. We also found a small percentage of non-additive epigenetic effects which might act as an evolutionary bet-hedging strategy and increase fitness under environmental change.

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Snapshot of DNA methylation changes associated with hybridization in Xenopus

Physiological Genomics ◽

10.1152/physiolgenomics.00110.2011 ◽

2011 ◽

Vol 43 (22) ◽

pp. 1276-1280 ◽

Cited By ~ 12

Author(s):

Alie Patrick Koroma ◽

Raymond Jones ◽

Pawel Michalak

Keyword(s):

Parental Species ◽

Principal Coordinate Analysis ◽

F1 Hybrids ◽

Epigenetic Changes ◽

Sterile Hybrid ◽

Control Gene ◽

Control Gene Expression ◽

Males And Females ◽

The Difference ◽

Methylation Patterns

Hybridization often results in dramatic genome reconfigurations including epigenetic changes that control gene expression. Here we survey methylation patterns of interspecific Xenopus F1 hybrids relative to parental species X. laevis and X. muelleri, using methyl-sensitive amplification polymorphisms (MSAPs). Out of a total of 546 MSAP markers, 364 were effective in elucidating the difference in methylation patterns between the hybrids and the parental species. Principal coordinate analysis of methylated fragments revealed four distinct clusters with the two parental species separate from hybrid males and females. On average, hybrids were characterized by a higher proportion (70.6%) of methylated fragments compared with the parental species (64.5%), and this difference was consistent with previously observed disruptions of hybrid transcriptomes. The proportion of methylated fragments did not correlate with variation in genome size, as measured with flow cytometry. The levels of methylation in sterile hybrid males (73.8%) were higher than in fertile hybrid females (68.6%), but this difference was not statistically significant. A total of 76 methylated fragments (20.9%) were hybrid-unique, presumably originating from methylation alterations in hybrid genomes.

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Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

Scientific Reports ◽

10.1038/s41598-021-93257-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Weitao Chen ◽

Ming Zou ◽

Yuefei Li ◽

Shuli Zhu ◽

Xinhui Li ◽

...

Keyword(s):

De Novo ◽

Parental Species ◽

F1 Hybrids ◽

Pelteobagrus Fulvidraco ◽

F1 Hybrid ◽

Short Reads ◽

Final Assembly ◽

Genome Complexity ◽

Hybrid Genome ◽

Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

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PrBn, a Major Gene Controlling Homeologous Pairing in Oilseed Rape (Brassica napus) Haploids

Genetics ◽

10.1093/genetics/164.2.645 ◽

2003 ◽

Vol 164 (2) ◽

pp. 645-653 ◽

Cited By ~ 4

Author(s):

Eric Jenczewski ◽

Frédérique Eber ◽

Agnès Grimaud ◽

Sylvie Huet ◽

Marie Odile Lucas ◽

...

Keyword(s):

Brassica Napus ◽

Oilseed Rape ◽

Chromosome Pairing ◽

Major Gene ◽

Major Effect ◽

F1 Hybrids ◽

Precise Control ◽

Ph1 Locus ◽

Likelihood Approach ◽

Likelihood Ratio Statistics

Abstract Precise control of chromosome pairing is vital for conferring meiotic, and hence reproductive, stability in sexually reproducing polyploids. Apart from the Ph1 locus of wheat that suppresses homeologous pairing, little is known about the activity of genes that contribute to the cytological diploidization of allopolyploids. In oilseed rape (Brassica napus) haploids, the amount of chromosome pairing at metaphase I (MI) of meiosis varies depending on the varieties the haploids originate from. In this study, we combined a segregation analysis with a maximum-likelihood approach to demonstrate that this variation is genetically based and controlled mainly by a gene with a major effect. A total of 244 haploids were produced from F1 hybrids between a high- and a low-pairing variety (at the haploid stage) and their meiotic behavior at MI was characterized. Likelihood-ratio statistics were used to demonstrate that the distribution of the number of univalents among these haploids was consistent with the segregation of a diallelic major gene, presumably in a background of polygenic variation. Our observations suggest that this gene, named PrBn, is different from Ph1 and could thus provide complementary information on the meiotic stabilization of chromosome pairing in allopolyploid species.

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GENOME SIZE IN THREE SPECIES OF Glandularia AND THEIR HYBRIDS

Journal of Basic and Applied Genetics ◽

10.35407/bag.2019.xxx.02.05 ◽

2019 ◽

Vol 30 (2) ◽

pp. 47-54

Author(s):

M.R. Ferrari ◽

E.J. Greizerstein ◽

L. Poggio

Keyword(s):

Genome Size ◽

Dna Content ◽

High Frequency ◽

Parental Species ◽

The Other ◽

F1 Hybrids ◽

Homoeologous Pairing ◽

The Relationship ◽

Species Being ◽

Homoeologous Chromosomes

In this work the relationship between genome size of Glandularia species and the meiotic configurations found in their hybrids are discussed. Glandularia incisa (Hook.) Tronc., growing in two localities of Corrientes and Córdoba provinces, Argentina, with different ecological conditions, showed inter-population variability of the 2C-value. The DNA content found in the Corrientes locality (2.41 pg) was higher than that obtained in the Córdoba locality (2.09 pg) which has more stressful environmental conditions than the former. These values are statistically different from those that were found in Glandularia pulchella (Sweet) Tronc. from Corrientes (1.43 pg) and in Glandularia perakii Cov. et Schn from Córdoba (1.47 pg). The DNA content of the diploid F1 hybrids, G. pulchella × G. incisa and G. perakii × G. incisa, differed statistically from the DNA content of the parental species, being intermediate between them. Differences in the frequency of pairing of homoeologous chromosomes were observed in the hybrids; these differences cannot be explained by differences in genome size since hybrids with similar DNA content differ significantly in their meiotic behavior. On the other hand, the differences in the DNA content between the parental species justify the presence of a high frequency of heteromorphic open and closed bivalents and univalents with different size in the hybrids. Key words: Intra-specific DNA content variability, homoeologous pairing, heteromorphic bivalents

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Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1912129116 ◽

2019 ◽

Vol 116 (48) ◽

pp. 24285-24295 ◽

Cited By ~ 16

Author(s):

Iradj Sobhani ◽

Emma Bergsten ◽

Séverine Couffin ◽

Aurélien Amiot ◽

Biba Nebbad ◽

...

Keyword(s):

Colorectal Cancer ◽

Bacterial Species ◽

Aberrant Crypt Foci ◽

Sporadic Colorectal Cancer ◽

Gene Promoters ◽

Normal Tissues ◽

Complex Interactions ◽

Dna Alterations ◽

Methylation Patterns ◽

Epigenetic Signatures

Sporadic colorectal cancer (CRC) is a result of complex interactions between the host and its environment. Environmental stressors act by causing host cell DNA alterations implicated in the onset of cancer. Here we investigate the stressor ability of CRC-associated gut dysbiosis as causal agent of host DNA alterations. The epigenetic nature of these alterations was investigated in humans and in mice. Germ-free mice receiving fecal samples from subjects with normal colonoscopy or from CRC patients were monitored for 7 or 14 wk. Aberrant crypt foci, luminal microbiota, and DNA alterations (colonic exome sequencing and methylation patterns) were monitored following human feces transfer. CRC-associated microbiota induced higher numbers of hypermethylated genes in murine colonic mucosa (vs. healthy controls’ microbiota recipients). Several gene promoters including SFRP1,2,3, PENK, NPY, ALX4, SEPT9, and WIF1 promoters were found hypermethylated in CRC but not in normal tissues or effluents from fecal donors. In a pilot study (n = 266), the blood methylation levels of 3 genes (Wif1, PENK, and NPY) were shown closely associated with CRC dysbiosis. In a validation study (n = 1,000), the cumulative methylation index (CMI) of these genes was significantly higher in CRCs than in controls. Further, CMI appeared as an independent risk factor for CRC diagnosis as shown by multivariate analysis that included fecal immunochemical blood test. Consequently, fecal bacterial species in individuals with higher CMI in blood were identified by whole metagenomic analysis. Thus, CRC-related dysbiosis induces methylation of host genes, and corresponding CMIs together with associated bacteria are potential biomarkers for CRC.

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Gene Flow Between Introduced and Native Eucalyptus Species: Morphological Analysis of Tri-Species and Backcross Hybrids Involving E. nitens

Silvae Genetica ◽

10.1515/sg-2007-0019 ◽

2007 ◽

Vol 56 (1-6) ◽

pp. 127-133 ◽

Cited By ~ 7

Author(s):

C. Barbour ◽

B. M. Potts ◽

R. E. Vaillancourt

Keyword(s):

Gene Flow ◽

Second Generation ◽

Current Work ◽

F1 Hybrids ◽

Morphological Identification ◽

Eucalyptus Species ◽

Pure Species ◽

Backcross Hybrids ◽

In The Wild ◽

Species Hybrids

Summary Morphometric analyses were conducted on second-generation tri-species and backcross hybrids in Eucalyptus. These hybrids were all produced using pollen from two E. nitens x cordata F1 hybrids and controlled pollination techniques. Tri-species hybrids were created with E. gunnii, E. ovata and E. viminalis as females, while backcrosses were produced with E. cordata. Multivariate analysis of seedling characteristics indicated that eighty percent of the backcross hybrids fell within the morphological range of E. cordata. All three cross combinations of the tri-species hybrids were biased away from E. nitens and towards their maternal parent and E. cordata. The inclusion of data for first-generation (F1) hybrids between the pure parental species in the current work showed the F1’s to be easily distinguishable from pure species, compared to second-generation hybrids. The use of morphology for detecting second-generation hybridisation involving exotic plantation species and native eucalypt populations will therefore be unreliable, and identifies a need for preventing second-generation hybrids from establish in the wild. The current work, nevertheless, provides further demonstration of the effectiveness of morphological identification of F1 hybrids. The easy recognition of F1 hybrids will be useful in identifying sites and species at risk of exotic gene flow and enable the development of weeding programs that focus on removing exotic hybrids in the wild.

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Patterns of Inheritance in the Bowing Display and Associated Behaviour of Some Hybrid Streptopelia Doves

Behaviour ◽

10.1163/156853970x00303 ◽

1970 ◽

Vol 36 (3) ◽

pp. 187-214 ◽

Cited By ~ 20

Author(s):

S.J.J.F. Davies

Keyword(s):

The Other ◽

F1 Hybrids ◽

Characteristic Form ◽

Pure Species ◽

F1 Hybrid ◽

Cine Film ◽

F2 Generation ◽

Species Hybrids ◽

Relative Variability

AbstractThe bowing display of Streptopelia doves was studied in captive individuals of five species at Madingley, Cambridge, England from 1961 to 1964. The five species were S. roseogrisea-(risoria) (barbary), S. decaocto (collared), S. turtur (turtle), S. chinensis (necklace) and S. senegalensis (senegal). F1 hybrids were bred between the barbary and the other four species and single males of each of the F1 necklace x collared and senegal x turtle were also observed. F2 generation birds of the collared x barbary F1 hybrid, as well as some backcrossed birds were included in the study. Bowing displays were usually given only by male doves when close to another dove. The form of the bowing display differed from species to species and exhibited a typical intensity in each species. Each hybrid also had a bowing display of characteristic form. The ciné film showed that there was variation in form between the bowing cycles of any one bout, both in the pure species and in the hybrids. This variation could not be adequately described from the films taken in this study. The rate of bowing of each species was constant and differed from that of every other species. Hybrids also exhibited a typical intensity in this character. There was much more intra-specific and intra-hybrid variaton in the timing of individual movements within bowing cycles in a bout than in the timing of the bowing cycle as a whole. The relative variability of the different elements could be ranked, and in all species and hybrids studied the timing of the total cycle tended to be least variable and that of the pause at the top of the bow most variable. The frequencies with which bowing displays and kah calls were given under standard conditions, were measured, and provided two other behavioural characters whose pattern of inheritance could be studied. Three patterns of inheritance were found in each of these behaviour patterns of the F1 hybrids. In some cases the behaviour was intermediate between that of the two parents, in others it approximated the behaviour of one parent closely and in others again the hybrid's behaviour exceeded the range of either parent.

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Patterns of evolution of genes disrupted in expression in Drosophila species hybrids

Genetics Research ◽

10.1017/s0016672305007500 ◽

2005 ◽

Vol 85 (2) ◽

pp. 119-125 ◽

Cited By ~ 12

Author(s):

MOHAMED A. F. NOOR

Keyword(s):

Amino Acid ◽

Parental Species ◽

Species Group ◽

Pure Species ◽

X Chromosomes ◽

Regulatory Pathways ◽

Regulatory Architecture ◽

Species Groups ◽

Male Specific ◽

Species Hybrids

Divergence between species in regulatory pathways may contribute to hybrid incompatibilities such as sterility. Consistent with this idea, genes involved in male fertility often evolve faster than most other genes both in amino acid sequence and in expression. Previously, we identified a panel of male-specific genes underexpressed in sterile male hybrids of Drosophila simulans and D. mauritiana relative to pure species, and we showed that this underexpression is associated with infertility. In a preliminary effort to assess the generalities in the patterns of evolution of these genes, I examined patterns of mRNA expression in three of these genes in sterile F1 hybrid males of D. pseudoobscura and D. persimilis. F1 hybrid males bearing D. persimilis X chromosomes underexpressed all these genes relative to the parental species, while hybrids bearing D. pseudoobscura X chromosomes underexpressed two of these three genes. Interestingly, the third gene, CG5762, has undergone extensive amino acid evolution within the D. pseudoobscura species group, possibly driven by positive natural selection. We conclude that some of the same genes exhibit disruptions in expression within each of the two species groups, which could suggest commonalities in the regulatory architecture of sterility in these groups. Alternative explanations are also considered.

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Molecular genetic evidence for allotetraploid hybrid speciation in the genus Crocus L. (Iridaceae)

Phytotaxa ◽

10.11646/phytotaxa.258.2.2 ◽

2016 ◽

Vol 258 (2) ◽

pp. 121 ◽

Cited By ~ 5

Author(s):

ÁGNES MOSOLYGÓ-L ◽

GÁBOR SRAMKÓ ◽

SÁNDOR BARABÁS ◽

LEVENTE CZEGLÉDI ◽

ANDRÁS JÁVOR ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Parental Species ◽

Molecular Genetic ◽

Parallel Evolution ◽

Carpathian Basin ◽

Hybrid Origin ◽

F1 Hybrids ◽

Aflp Data ◽

F1 Hybrid

Although dysploidy and polyploidisation events are known to be important drivers in the evolutionary history of the genus Crocus, only a few examples of natural hybrid origins have so far been documented. Here, we describe the phylogenetic affinities of five taxa in the Crocus vernus species complex from the Carpathian Basin in Central Europe. Genetic variability was evaluated using chloroplast DNA sequences of the accD-psaI intergenic spacer and amplified fragment length polymorphism (AFLP) in combination with karyological observations. Genetic diversity and differentiation of the seven investigated Crocus species were also evaluated using AFLP data. We created a phylogenetic hypothesis using both sequences and AFLP fingerprinting data under maximum parsimony (MP). AFLPs were also analysed by means of multivariate statistics using principal coordinate (PCoA) analysis and Bayesian clustering (BC) to test for hybridity. Both the AFLP and plastid phylogenetic trees separated the taxa into two groups: (1) a ‘Balkan’ clade, and; (2) an ‘Adriatic’ clade. The Balkan clade contained Crocus heuffelianus samples and one Crocus vittatus from Croatia as well as Crocus tommasinianus samples from Hungary; the Adriatic clade included Crocus vittatus and Crocus vernus samples from Hungary and Croatia as well as Crocus neapolitanus from Italy. A hard incongruence was found in the placement of the Slovakian Crocus scepusiensis which clustered inside the Balkan clade on our plastid tree, while it fell in the Adriatic clade on the AFLP tree. The same populations occupied intermediate position on the PCoA plot. The BC analysis assigned all Crocus scepusiensis specimens as F1 hybrids, while Crocus vernus and Crocus heuffelianus were assigned as parental species. Together with our cytological investigation that determined a 2n=18 chromosome number of Crocus scepusiensis, we conclude an allopolyploid hybrid origin for this Northern Carpathian taxon as the result of a cross between members of the 2n=10 Balkan clade (e.g., Crocus heuffelianus from Transylvania) and the 2n=8 Adriatic clade (Crocus vernus). A similar origin is postulated for the North Balkan Crocus vittatus (2n=18), which was clustered as an F1 hybrid in the BC analysis; thus, parallel evolution may have taken place in the northern and southern part of the Carpathian Basin beginning from the same parental species but leading to different allopolyploid derivatives.

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Gene flow between introduced and native Eucalyptus species: crossability of native Tasmanian species with exotic E. nitens

Australian Journal of Botany ◽

10.1071/bt05021 ◽

2005 ◽

Vol 53 (5) ◽

pp. 465 ◽

Cited By ~ 15

Author(s):

R. C. Barbour ◽

B. M. Potts ◽

R. E. Vaillancourt

Keyword(s):

Gene Flow ◽

Native Species ◽

Seed Set ◽

Pollen Competition ◽

F1 Hybrids ◽

Eucalyptus Species ◽

F1 Hybrid ◽

Genetic Pollution ◽

Morphometric Analyses ◽

Natural Hybridisation

Eucalyptus nitens (Deane & Maiden) Maiden has been extensively introduced to the island of Tasmania for plantation purposes. Natural hybridisation with two native species has already been confirmed and this study aimed to determine which other Tasmanian native species could potentially hybridise with E. nitens. Controlled and supplementary pollinations with E. nitens pollen were undertaken on all Tasmanian native species that are potentially at risk of exotic gene flow and hence genetic pollution. Across the seven species tested by using controlled pollinations, seed set per flower, following E. nitens pollinations, was significantly less than for intraspecific outcross pollinations. No significant differences were evident in the percentage of seed that germinated or the percentage of germinants that grew into healthy seedlings in the glasshouse. Hybridity was verified by morphometric analyses and F1 hybrid seedlings were clearly differentiated from parental species and generally intermediate in morphology. Supplementary E. nitens pollination of open-pollinated native flowers was conducted to simulate natural pollination where pollen competition would occur. Seven of the fifteen species tested produced F1 hybrids in this case; however, further crossing is required to verify failed cross combinations. Although E. nitens can potentially hybridise with many native species, the results from both supplementary and controlled pollinations suggest the presence of post-pollination barriers of varying strength that need to be considered in assessing the risk of exotic gene flow from plantations.

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