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Results for “Genetic Introgression”

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PubMed2000

The kdr mutation occurs in the Mopti form of Anopheles gambiae s.s. through introgression.

Anopheles gambiae s.s. is a complex of sibling taxa characterized by various paracentric inversions. In west and central Africa, where several taxa are sympatric, a kdr mutation responsible for pyrethroid resistance has been described in only one (the S taxon), suggesting an absence of gene flow between them. Following a thorough sampling, we have found a kdr mutation in another taxon (M). To establish whether this mutation is the same event or not, the large intron upstream of the kdr mutation was sequenced to find polymorphic sites in susceptible/resistant and M/S mosquitoes. The low genetic diversity found in this DNA region indicates that a local genetic sweep has recently occurred. However, some polymorphic sites were found, and it is therefore concluded that the kdr mutation in the M taxon is not an independent mutation event, and is best explained by an introgression from the S taxon. These results are discussed within the context of possible gene flow between members of An. gambiae s.s. taxa, and with the possible spread of the kdr mutation in other closely related malaria vectors of the An. gambiae complex.

Africa↗

PubMed1999

Linkage disequilibrium mapping of molecular polymorphisms at the scabrous locus associated with naturally occurring variation in bristle number in Drosophila melanogaster.

We evaluated the hypothesis that the Drosophila melanogaster second chromosome gene scabrous (sca), a candidate sensory bristle number quantitative trait locus (QTL), contributes to naturally occurring variation in bristle number. Variation in abdominal and sternopleural bristle number was quantified for wild-derived sca alleles in seven genetic backgrounds: as homozygous second chromosomes (C2) in an isogenic background, homozygous lines in which approximately 20 cM including the sca locus had been introgressed into the isogenic background (sca BC), as C2 and sca BC heterozygotes and hemizygotes against a P element insertional sca allele and a P-induced sca deficiency in the same isogenic background, and as sca BC heterozygotes against the wild-type sca allele of isogenic strain. Molecular restriction map variation was determined for a 45 kb region including the sca locus, and single-stranded conformational polymorphism (SSCP) was examined for the third intron and parts of the third and fourth exons. Associations between each of the 27 molecular polymorphisms and bristle number were evaluated within each genotype and on the first principal component score determined from all seven genotypes, separately for each sex and bristle trait. Permutation tests were used to assess the empirical significance thresholds, accounting for multiple, correlated tests, and correlated markers. Three sites in regulatory regions were associated with female-specific variation in abdominal bristle number, one of which was an SSCP site in the region of the gene associated with regulation of sca in embryonic abdominal segments.

Animals↗

PubMed2002

Substitution of Dmo1 with normal alleles results in decreased manifestation of diabetes in OLETF rats.

AIM: Dmo1 (Diabetes Mellitus OLETF type I) is a major quantitative trait locus for dyslipidaemia, obesity and diabetes phenotypes in the Otsuka Long Evans Tokushima Fatty (OLETF) rat strain. To evaluate possible metabolic and pathological improvements generated by correction of the Dmo1 genetic pathway, we produced congenic lines, in which both OLETF Dmo1 alleles are replaced by the F344-derived genome. METHODS: Congenic animals were produced by introgressing F344-derived Dmo1 alleles into the OLETF rat. Congenic animals of the fourth generation (BC4) were intercrossed to obtain F1 animals (BC4:F1). Animals of the next generation, BC4:F2, were used for this study. We used 23 BC4:F2 males harbouring homozygous replacement of the OLETF Dmo1 region with the F344-derived genome. Seven animals with OLETF-derived Dmo1 alleles were used as controls. RESULTS: Dmo1-F344/F344 congenic rats showed significant decreases in body weight, abdominal fat weight, serum triacylglycerols, total cholesterol, food consumption and blood glucose after glucose loading (13%, 39%, 45%, 27%, 18% and 27% respectively; p < 0.05) compared with Dmo1-OLETF/OLETF animals. Furthermore, histopathological analysis of the kidney showed that mesangial sclerosis, hyalin deposits and deposition of PAS-positive substance were significantly lower in Dmo1-F344/F344 animals (p < 0.05). CONCLUSION: Improvements in metabolic parameters and histopathological scores show that correction of the Dmo1 genetic pathway in the diabetic and mildly obese OLETF rat strain produces wide-ranging therapeutic effects. Thus, this pathway might represent a new drug target also applicable to humans.

Animals↗

PubMed2003

Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. III. Heterogeneous accumulation of hybrid incompatibilities, degree of dominance, and implications for Haldane's rule.

The genetic basis of Haldane's rule was investigated through estimating the accumulation of hybrid incompatibilities between Drosophila simulans and D. mauritiana by means of introgression. The accumulation of hybrid male sterility (HMS) is at least 10 times greater than that of hybrid female sterility (HFS) or hybrid lethality (HL). The degree of dominance for HMS and HL in a pure D. simulans background is estimated as 0.23-0.29 and 0.33-0.39, respectively; that for HL in an F1 background is unlikely to be very small. Evidence obtained here was used to test the Turelli-Orr model of Haldane's rule. Composite causes, especially, faster-male evolution and recessive hybrid incompatibilities, underlie Haldane's rule in heterogametic male taxa such as Drosophila (XY male and XX female). However, if faster-male evolution is driven by sexual selection, it contradicts Haldane's rule for sterility in heterogametic-female taxa such as Lepidoptera (ZW female and ZZ male). The hypothesis of a faster-heterogametic-sex evolution seems to fit the current data best. This hypothesis states that gametogenesis in the heterogametic sex, instead of in males per se, evolves much faster than in the homogametic sex, in part because of sex-ratio selection. This hypothesis not only explains Haldane's rule in a simple way, but also suggests that genomic conflicts play a major role in evolution and speciation.

Animals↗

PubMed2003

Use of SSRs for establishing heterotic groups in subtropical maize.

Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objectives of our research were to: (1) investigate the relationship of simple sequence repeats (SSR) based genetic distances between populations and panmictic midparent heterosis (PMPH) in a broad range of CIMMYT maize germplasm, (2) evaluate the usefulness of SSR markers for defining heterotic groups and patterns in subtropical germplasm, and (3) examine applications of SSR markers for broadening heterotic groups by systematic introgression of other germplasm. Published data of two diallels and one factorial evaluated for grain yield were re-analyzed to calculate the PMPH in population hybrids. Additionally, 20 pools and populations widely used in CIMMYT's breeding program were assayed with 83 SSR markers covering the entire maize genome. Correlations of squared modified Roger's distance (MRD(2)) and PMPH were mostly positive and significant, but adaption problems caused deviations in some cases. For intermediate- and early-maturity subtropical germplasm, two heterotic groups could be suggested consisting of a flint and dent composite. We concluded that the relationships between the populations obtained by SSR analyses are in excellent agreement with pedigree information. SSR markers are a valuable complementation to field trials for identifying heterotic groups and can be used to introgress exotic germplasm systematically.

Alleles↗

PubMed2006

Microsatellites reveal extensive geographical, ecological and genetic contacts between invasive and indigenous whitefly biotypes in an insular environment.

Human-mediated bioinvasions provide the opportunity to study the early stages of contact between formerly allopatric, divergent populations of a species. However, when invasive and resident populations are morphologically similar, it may be very difficult to assess their distribution in the field, as well as the extent of ecological overlap and genetic exchanges between invasive and resident populations. We here illustrate the use of data obtained from a set of eight microsatellite markers together with Bayesian clustering methods to document invasions in a group of major tropical pests, Bemisia tabaci, which comprises several morphologically indistinguishable biotypes with different agronomic impacts. We focus on the island of La Réunion, where an invasive biotype (B) has recently been introduced and now interacts with the resident biotype (Ms). The temporal and spatial distribution, host-plant range and genetic structure of both biotypes are investigated. We showed (i) that, without prior information, clustering methods separate two groups of individuals that can safely be identified as the B and Ms biotypes; (ii) that the B biotype has invaded all regions of the island, and showed no signs of genetic founder effect relative to the Ms biotype; (iii) that the B and Ms biotypes coexist in sympatry throughout most of their geographical ranges, although they tend to segregate into different host plants; and finally (iv) that asymmetrical and locus-specific introgression occurs between the two biotypes when they are in syntopy.

Animals↗

PubMed2005

When morphometry meets genetics: inferring the phylogeography of Carabus solieri using Fourier analyses of pronotum and male genitalia.

Population differentiation is a crucial step in the speciation process and is therefore a central subject in studies of microevolution. Assessing divergence and inferring its dynamics in space and time generally require a wide array of markers. Until now however, most studies of population structure are based on molecular markers and those concerning morphological traits are more scarce. In the present work, we studied morphological differentiation among populations of the ground beetle Carabus solieri, and tested its congruence with genetic population structure. The shape of pronotum and aedeagus was assessed using Dual Axis Fourier Shape Analysis. manova on Fourier coefficients revealed highly significant morphological variation between populations and a similar geographical pattern of differentiation for both structures. On the whole, morphological and genetic patterns were also found to be congruent. Our analysis confirms the phylogeographical scenario proposing that two entities of C. solieri differentiated during the last glaciation events before recolonizing the actual range of the species. It also indicates a large introgression between the two differentiated entities in the centre of the range.

Analysis of Variance↗

PubMed2002

Ancient versus reticulate origin of a hemiclonal lineage.

Crossing experiments revealed that a diploid hybridogenetic fish (genus Poeciliopsis) from the Río Mocorito (Sinaloa, Mexico) is trihybrid. Its haploid maternal genome is inherited clonally (i.e., hemiclonally), and it expresses a mixture of morphological traits found in the closely related species P. monacha and P. viriosa. Its haploid paternal genome is replaced in each generation by mating with males of a more distantly related sexual species, P. lucida. However, expression of mixed (monacha X viriosa) traits by this hemiclone is also consistent with retention of shared ancestral polymorphisms. If true, this hemiclonal lineage would be one of the few examples of an ancient asexual taxon. We used mitochondrial DNA and allozymes to test whether the maternal progenitor of the Mocorito hybridogen was a recent P. monacha X P. viriosa hybrid or a remnant of their most recent common ancestor. Our results clearly link the hemiclonal genome to contemporary P. monacha and therefore support the hypothesis of a recent origin. Additionally, our findings suggest that this unisexual fish may serve as a vehicle for introgression between two allopatric sexual species.

Animals↗

PubMed2002

AFLP markers and cytotaxonomic analysis reveal hybridisation in the genus Schoenus (Cyperaceae).

Molecular, cytological, and morphological data support the existence of a hybrid population between Schoenus nigricans and Schoenus ferrugineus. This population was found in northeastern Italy, where S. nigricans is central with respect to its natural range and S. ferrugineus is marginal, being most common in the Alps and in central and northern Europe. Molecular marker data show that the putative hybrid population is genetically intermediate between nearby populations of the parent species. Cytological evidence confirmed the hybrid nature of this population, as does the almost complete sterility of plants within the population. Although no seeds were produced by the hybrid population, some possibly fertile pollen grains were produced; this suggests that the possibility of introgression between the two species through the hybrids cannot completely be excluded.

Crosses, Genetic↗

PubMed1993

[Genome diagnosis in domestic animals].

Different contributions to the development and applications of genomic diagnosis methods in domestic animals are reported. DNA fingerprints were used to solve parentage disputes in different species, and to reveal leucochimerism in bovine dizygotic twins. In cattle, an embryo sexing method and a freemartinism diagnosis assay were also developed. The search for molecular markers of the MH (muscular hypertrophy) and R (rouan) bovine genes is described. Prion protein gene polymorphisms are investigated in the framework of a research on the genetics of bovine spongiform encephalopathies. The mutation responsible for the autosomal recessive lethal condition BLAD (bovine leucocyte adhesion deficiency) in Holstein cattle is found in our country, and the carries can be detected by a molecular method. The mutation responsible for the halothane sensitivity in pig can also be detected, what is done to control efficiently the introgression of the stress resistance allele in a Piétrain strain.

Animals↗

PubMed1996

Distinguishing between primary and secondary intergradation among morphologically differentiated populations of Anolis marmoratus.

Distinguishing between primary and secondary intergradation among differentiated populations, and the relative importance of drift and selection, are persistent problems in evolutionary biology. An historical perspective on population interactions can provide insight into the nature of contacts, and thus help resolve these questions. Continuously distributed populations of Anolis marmoratus from the island of Basse Terre in the Guadeloupean archipelago of the Lesser Antilles show a striking degree of geographic variation in morphology. Initial surveys of mtDNA variation from throughout the Guadeloupean Archipelago revealed one case where levels of sequence difference and phylogenetic relationships of alleles from morphologically differentiated populations from the east coast of Basse Terre were consistent with primary intergradation. In this paper, I examine the genetic population structure of a series of populations spanning this north-south cline in morphological variation to test the hypothesis of primary intergradation. Sequences of the mitochondrial cytochrome-b gene from 50 individuals representing five populations spanning the cline were obtained and fourteen unique haplotypes (differing by 2% or less) were detected. Patterns of nucleotide substitution among haplotypes do not deviate from neutral expectation indicating no effect of selection at the level of mtDNA sequences. Estimates of population structure and gene flow were made using both summary statistics for nucleotide diversity (Nst) and cladistic methods. The results are sensitive to the choice of gene flow model, and this is discussed in detail. Mitochondrial variation in the northern populations may not be at equilibrium, and the phylogeny of alleles is consistent with a recent increase in effective population size. Estimates of nucleotide diversity, gene flow, and the phylogenetic relationships of haplotypes indicate that the southern-most population (representing the extreme of morphological variation along this cline) has been relatively isolated from populations to the north and has experienced a reduced effective population size. The apparent clinal variation between the southern population and the others may therefore reflect secondary contact and introgression rather than primary intergradation.

Animals↗

PubMed2002

Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza Rufipogon Griff., into indica rice (Oryza sativa L.).

This study was conducted to identify and map the quantitative trait locus (QTL) controlling Al tolerance in rice using molecular markers. A population of 171 F(6) recombinant inbred lines (RILs) derived from the cross of Oryza sativa (IR64), the Al susceptible parent, and Oryza rufipogon, the Al tolerant parent, was evaluated for Al tolerance using a nutrient solution with and without 40 ppm of active Al(+3). A genetic map, consisting of 151 molecular markers covering 1,755 cM with an average distance of 11.6 cM between loci, was constructed. Nine QTLs were dentified including one for root length under non-stress conditions (CRL), three for root length under Al stress (SRL) and five for relative root length (RRL). O. rufipogon contributed favorable alleles for each of the five QTLs for RRL, which is a primary parameter for Al tolerance, and individually they explained 9.0-24.9% of the phenotypic variation. Epistatic analysis revealed that CRL was conditioned by an epistatic effect, whereas SRL and RRL were controlled by additive effects. Comparative genetic analysis showed that QTLs for RRL, which mapped on chromosomes 1 and 9, appear to be consistent among different rice populations. Interestingly, a major QTL for RRL, which explained 24.9% of the phenotypic variation, was found on chromosome 3 of rice, which is conserved across cereal species. These results indicate the possibilities to use marker-assisted selection and pyramiding QTLs for enhancing Al tolerance in rice. Positional cloning of such QTLs introgressed from O. rufipogon will provide a better understanding of the Al tolerance mechanism in rice and the evolutionary genetics of plant adaptation to acid-soil conditions across cereal species.

Alleles↗

PubMed2006

The introgression of chromosome 6P specifying for increased numbers of florets and kernels from Agropyron cristatum into wheat.

A wheat (Triticum aestivum L.) line 4844 with superior numbers of florets and grains per spike was derived from the cross between Fukohokomugi wheat and Agropyron cristatum (L.) Gaertn. In order to determine the genetic control of floret and kernel number per spike in this line, chromosome addition and substitution lines that were derived from line 4844 were characterized by means of in situ hybridization, microsatellite (SSR), and gliadin analyses. Genomic in situ hybridization analysis with biotinylated P genomic DNA of A. cristatum as a probe demonstrated that the increased number of florets and grains in a spike was associated with the introgression of an A. cristatum chromosome. Fluorescence in situ hybridization, using a repetitive sequence, pAs1, derived from Aegilops squarrosa L., indicated the replacement of chromosome 6D of wheat in the wheat-A. cristatum chromosome substitution lines. This was confirmed by microsatellite analyses with wheat SSR markers specific for chromosome 6D, suggesting that the A. cristatum chromosome was homoeologous to group 6 and was therefore designated as 6P. This conclvsion was further confirmed by amplification using EST-SSR markers and gliadin analysis. The increased number of florets and kernels within a spike of the wheat-A. cristatum hybrids thus was controlled by gene(s) located on A. cristatum chromosome 6P.

Agropyron↗

PubMed2004

Clinal genetic variation and the 'rare allele phenomenon' in random mating populations of Urophora cardui (Diptera: Tephritidae).

In the present study we investigate a contact zone between two population groups of the tephritid fly Urophora cardui. We investigate scenarios that may have produced the genetic differentiation of the two groups, and we describe the 'rare allele phenomenon' from the contact zone. The rare allele phenomenon refers to alleles that are found at high frequency in contact zones but are rare or lacking outside the contact zone. The phenomenon is often observed in hybrid zones between subspecies of limited reproductive compatibility, but seldom in populations with random mating. Clinal genetic variation was observed at three loci in the contact zone. Three alleles at the locus Aat showed steep clines, between 20-70 km wide. A rare Aat-A allele occurred at high frequency in the centre of the contact zone. Two further loci, Hk and Pgd, showed less steep clinal genetic variation, the transition being in and slightly south of the centre of the Aat cline. Populations showed Hardy-Weinberg proportions and there was no evidence for linkage disequlibrium. These findings suggest random mating and gradual introgression between the population systems, which may originate from at least two range expansions. Aat's steep clines and rare allele may indicate selection on Aat alleles, although we presently can not quantify any agents. Because U. cardui experiences random mating in the contact zone with no apparent 'hybrid' incompatibility, mating experiments offer the possibility for future enquiries about the genetic basis of the rare allele phenomenon.

Alleles↗

PubMed2005

Colonization, dispersal, and hybridization influence phylogeography of North Atlantic sea urchins (Strongylocentrotus droebachiensis).

We used frequency-based and coalescent-based phylogeographic analysis of sea urchin (Strongylocentrotus droebachiensis) mitochondrial DNA (mtDNA) sequences and previously published microsatellite data to understand the relative influence of colonization and gene flow from older (north Pacific) and younger (northeast Atlantic) sea urchin populations on genetic variation in the northwest Atlantic. We found strong evidence of survival of northwestern Atlantic populations in local Pleistocene glacial refugia: most haplotypes were the same as or closely related to Pacific haplotypes, with deep gene genealogies that reflect divergence times within the northwestern Atlantic that are much older than the last glacial maximum. We detected gene flow across the North Atlantic in the form of haplotypes shared with or recently descended from European populations. We also found evidence of significant introgression of haplotypes from a closely related species (S. pallidus). The relative magnitude of gene flow estimated by coalescent methods (and the effective population size differences among oceanic regions) depended on the genetic marker used. In general, we found very small effective population size in the northeastern Atlantic and high trans-Arctic gene flow between the Pacific and northwestern Atlantic. Both analyses suggested significant back-migration to the Pacific. However, microsatellites more strongly reflected older Pacific migration (with similar effective population sizes across the Arctic), whereas mtDNA sequences appeared to be more sensitive to recent trans- Atlantic dispersal (with larger differences in effective population size). These differences across marker types might have several biological or methodological causes, and they suggest caution in interpretation of the results from a single locus or class of markers.

Animals↗

PubMed2004

Autosomal differences between males and females in hybrid zones: a first report from Barbus barbus and Barbus meridionalis (Cyprinidae).

Narrow hybrid zones are generally subjected to the action of two forces: dispersal, which tends to homogenise the hybridising taxa, and selection against hybrids, which, in contrast, produces steep clines of introgression for diagnostic markers. Although differences between sexes in dispersal abilities or in susceptibility to hybrid counterselection are common in hybrid zones, autosomal genetic differences between males and females have never been reported to our knowledge. Barbus barbus and Barbus meridionalis (Cyprinidae) form a hybrid zone along the Lergue river. By carrying out a genetic analysis of males and females in six samples from two central stations of the hybrid zone using codominant markers (six allozymes and four microsatellite loci), we revealed significant multilocus and monolocus differences between the sexes. This could reflect a genetic difference among sexes within a same cohort, caused either by a survival (or fertility) differential among sexes or by a sex-specific pattern of dispersal. Alternatively, this may be due to genetic differentiation between cohorts, since male and female barbel exhibit different maturation, growth and survival patterns leading to different age distributions among sexes, and particularly among reproducers.

Age Factors↗

PubMed2025

G4SNVHunter: An R/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm.

G-quadruplexes (G4s) are nucleic acid secondary structures with important regulatory functions. Single-nucleotide variants (SNVs), one of the most common forms of genetic variation, can potentially impact the formation of G4 structures if they occur within G4 regions. However, there is currently a lack of software tools specifically designed to assess such effects. Here, we present an R/Bioconductor package named G4SNVHunter, which enables rapid detection of variants that may disrupt G4 structures. This tool, based on the core principles of the G4Hunter algorithm, can provide precise quantitative assessment of the propensity for G4 formation within genomic sequences. Specialized experimental methods can then be designed based on the results provided by G4SNVHunter to further verify the specific functions of the affected G4 structures, facilitating deeper insights into the biological impacts of genetic variants from the perspective of G4 structures. To showcase the functionality of the G4SNVHunter package, we analyzed the Neandertal and Denisovan archaic introgressed variants detected by the Sprime software, and identified approximately 5,800 variants located within G4 regions, among which around 230 may impair G4 structure formation propensity. The source code for the G4SNVHunter package has been publicly released under the MIT license at https://github.com/rongxinzh/G4SNVHunter and https://bioconductor.org/packages/devel/bioc/html/G4SNVHunter.html.

G-Quadruplexes↗

PubMed1984

Hybridization and introgression among species of sunfish (Lepomis): analysis by mitochondrial DNA and allozyme markers.

We explore the potential of mitochondrial DNA (mtDNA) analysis, alone and in conjunction with allozymes, to study low-frequency hybridization and introgression phenomena in natural populations. MtDNAs from small samples of nine species of sunfish (Lepomis, Centrarchidae) were purified and digested with each of 13 informative restriction enzymes. Digestion profiles for all species were highly distinct: estimates of overall fragment homology between pairs of species ranged from 0-36%. Allozymes encoded by nine nuclear genes also showed large freqency differences among species and together with mtDNA provided many genetic markers for hybrid identification. A genetic analysis of 277 sunfish from two locations in north Georgia revealed the following: (1) a low frequency of interspecific hybrids, all of which appeared to be F1's; (2) the involvement of five sympatric Lepomis species in the production of these hybrids; (3) no evidence for introgression between species in our study locales (although for rare hybridization, most later-generation backcrosses would not be reliably distinguished from parentals); (4) a tendency for hybridizations to take place preferentially between parental species differing greatly in abundance; (5) a tendency for the rare species in a hybrid cross to provide the female parent. Our data suggest that absence of conspecific pairing partners and mating stimuli for females of rarer species may be important factors in increasing the likelihood of interspecific hybridization. The maternal inheritance of mtDNA offers at least two novel advantages for hybridization analysis: (1) an opportunity to determine direction in hybrid crosses; and (2) due to the linkage among mtDNA markers, an increased potential to distinguish effects of introgression from symplesiomorphy or character convergence.

Animals↗