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Results for “Haplotype structures”

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PubMed2015

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Adaptation, Biological↗

PubMed1997

Genetic population structure in the yellow mongoose, Cynictis penicillata.

Phylogeographic structure was determined for the yellow mongoose, Cynictis penicillata, using mtDNA RFLPs and control region sequences. The RFLP analysis revealed 13 haplotypes which showed weak geographical patterning consistent with a recent range expansion from a refugial population(s). An analysis of molecular variance (AMOVA) revealed no correspondence between mtDNA phylogeography and subspecies delimitation, nor between matrilines and areas characterized by a high incidence of the viverrid-type rabies, of which the yellow mongoose is the principal vector. The lack of structure was also shown by control region sequences although four of the maternal lineages shared a near-perfect 81 bp repeat. We speculate that regional hot spots of the viverrid rabies biotype reflect population density differences in the yellow mongoose that are not underscored by genetic partitioning, at least at the level of resolution provided by our analyses.

Animals↗

PubMed2002

The hidden matrilineal structure of a solitary lemur: implications for primate social evolution.

Kin selection affects many aspects of social behaviour, especially in gregarious animals in which relatives are permanently associated. In most group-living primates with complex social behaviour, females are philopatric and organized into matrilines. Models of primate social evolution assume that females in solitary primates are also organized into matrilines. We examined the genetic structure and the mating system of a population of Coquerel's dwarf lemur (Mirza coquereli), a solitary primate from Madagascar, to test this assumption. Our genetic and behavioural analyses revealed that this population of solitary individuals is indeed structured into matrilines, even though this pattern was not predicted by behavioural data. Specifically, females sharing a mitochondrial DNA haplotype were significantly clustered in space and the average genetic and geographical distances among them were negatively correlated. Not all females were philopatric, but there is no evidence for the successful settlement of dispersing females. Although not all adult males dispersed from their natal range, they were not significantly clustered in space and all of them roamed widely in search of oestrous females. As a result, paternity was widely spread among males and mixed paternities existed, indicating that scramble competition polygyny is the mating system of this species. Our data therefore revealed facultative dispersal in both sexes with a strong bias towards female philopatry in this primitive primate. We further conclude that complex kinship structures also exist in non-gregarious species, where their consequences for social behaviour are not obvious.

Animals↗

PubMed1978

Immune responses of inbred guinea pigs and mice to helical sequential polymers of amino acids.

The immune responses against the sequential polypeptides; (T-G-A-Gly)n, (T-A-G-Gly)n, (Phe-G-A-Gly)n and (Phe-A-G-Gly)n were studied in inbred guinea pigs and mice. Strain 13 guinea pigs responded to (Phe-G-A-Gly)n and (T-G-A-Gly)n whereas strain 2 guinea pigs responded to (T-A-G-GLY)n and (Phe-A-G-Gly)n. These responses which are linked to MHC, are only against the helical form of the polymers which have conformational determinants. Significant cross reactions at the humoral and T cell levels (PELS) are exhibited with the following reciprocal combinations: (Phe-G-A-Gly)n and (T-G-A-Gly)n; (T-A-G-Gly)n and (Phe-A-G-Gly)n. With mice, the polymers were shown to be T dependent with the following response patterns: mice of H-2b haplotype respond against (T-G-A-Gly)n; those of H-2b, f and r haplotypes respond against (T-A-G-Gly)n. There are no responders against (Phe-G-A-Gly)n and only mice of H-2f respond against (Phe-A-G-Gly)n. "Nonresponders" respond against the MBSA aggregates of all of these polymers. The Ir gene(s) controlling these T cell dependent H-linked responses mapped to the IA subregion. Antibody responses against (T-G-A-Gly) and (T-A-G-Gly) were quite variable, and were most marked in, F1 mice of (responder and nonresponder) and in backcross populations of (F1 x R) and (F1 x NR). However, the T cell proliferative responses performed with nylon wool purified T cells gave clear cut and predictable distinctions between "responders" and nonresponders and linkage with responding haplotype. Hypotheses advanced to explain these findings relate to the poor immunogenicity (antibody) of these polymers, which have a restricted number of repeating determinants, the B cell mitogenic properties of these polymers and the possible involvement of suppressor cells. The specificities of the humoral responses, i.e. cross reactions, were similar to those found in guinea pigs. However, in contrast to the guinea pig studies cross stimulation with structurally related polymers occurred only in those situations where the immunizing and "crossreacting" polymers were both immunogenic in mice of the same haplotype, i.e., (T-A-G-Gly)n and (Phe-A-G-Gly)n in mice of H-2f haplotypes.

Animals↗

PubMed2005

Hidden diversity and host specificity in cycliophorans: a phylogeographic analysis along the North Atlantic and Mediterranean Sea.

In order to elucidate the evolutionary history and the population structure of the members of the phylum Cycliophora, which live commensally on three species of lobsters, we studied sequence variation in the mitochondrial gene cyctochrome c oxidase subunit I. Overall 242 sequences from 16 locations on both coasts of the North Atlantic, including the North Sea and the Mediterranean, were analysed, revealing 28 haplotypes, with a maximum sequence divergence of 16.6%. Total genetic diversity was high (h = 0.8322, pi = 0.0898), as it was for the commensals on Homarus americanus (17 haplotypes, h = 0.7506, pi = 0.0504). However, it was low for commensals on Nephrops norvegicus (6 haplotypes, h = 0.3899, pi = 0.0035), and intermediate for cycliophorans on Homarus gammarus (5 haplotypes, h = 0.3020, pi = 0.0140). Although two of the host lobsters co-inhabit the coastal waters of Europe, a strong genetic structure (78.45% of the observed genetic variation) was detected among populations on all host species, indicating the existence of a reproductively isolated species on each lobster. In addition, genetic structure over long distances exists among populations on each host species. Such patterns can be explained by the limited dispersal ability of the cycliophoran chordoid larva. Demographic and phylogenetic analyses suggest old and possibly cryptic populations present on H. americanus and H. gammarus, while the latter may have experienced recent bottlenecks, perhaps during Pleistocene glaciations. Populations on N. norvegicus appear to be of recent origin.

Animals↗

PubMed2001

Reelin gene alleles and haplotypes as a factor predisposing to autistic disorder.

Autistic disorder (MIM 209850) is currently viewed as a neurodevelopmental disease. Reelin plays a pivotal role in the development of laminar structures including the cerebral cortex, hippocampus, cerebellum and of several brainstem nuclei. Neuroanatomical evidence is consistent with Reelin involvement in autistic disorder. In this study, we describe several polymorphisms identified using RNA-SSCP and DNA sequencing. Association and linkage were assessed comparing 95 Italian patients to 186 ethnically-matched controls, and using the transmission/disequilibrium test and haplotype-based haplotype relative risk in 172 complete trios from 165 families collected in Italy and in the USA. Both case-control and family-based analyses yield a significant association between autistic disorder and a polymorphic GGC repeat located immediately 5' of the reelin gene (RELN) ATG initiator codon, as well as with specific haplotypes formed by this polymorphism with two single-base substitutions located in a splice junction in exon 6 and within exon 50. Triplet repeats located in 5' untranslated regions (5'UTRs) are indicative of strong transcriptional regulation. Our findings suggest that longer triplet repeats in the 5'UTR of the RELN gene confer vulnerability to autistic disorder.

Adult↗

PubMed1995

Nucleotide sequence analysis of the apolipoprotein B 3' VNTR.

Variable number of tandem repeat (VNTR) loci typically exhibit high rates of germline mutations that alter allele length and thus are ideal models for examining processes governing repeat sequence instability. We have characterized by nucleotide sequencing the internal structure of the apolipoprotein B (Apo B) 3' VNTR in a sample of same- and different-sized alleles previously associated with flanking marker haplotypes. Significant linkage disequilibrium between flanking polymorphisms and minisatellite alleles excludes unequal recombination as the predominant mechanism of mutation at the Apo B VNTR and is consistent with intra-allelic mutational processes such as replication slippage and/or unequal sister chromatid exchange. Diversity among different length alleles was distinctly polar and was usually attributable to changes in copy number at one particular repeat sequence. Analysis of predicted secondary structures for the dimeric repeats demonstrated a relationship between variability and the potential to form self-complementary intermediates. Preferential instability of the variable repeat: (i) was a function of its location within the tandem array; (ii) was not solely dependent on copy number; and (iii) may be related to the base composition of the VNTR and the degree of self-complementarity between the dimeric repeat sequences. The data suggest that polarized variability may be independent of the mutational process(es) generating length variation at minisatellite loci and suggest a possible alternative mechanism of mutation that involves the formation of secondary structures.

Alleles↗

PubMed2003

Mitochondrial differentiation in a polymorphic land snail: evidence for Pleistocene survival within the boundaries of permafrost.

The genetic differentiation of populations having colonized formerly unsuitable habitats after the Pleistocene glaciations depends to a great extent on the speed of expansion. Slow dispersers maintain their refugial diversity whereas fast dispersal leads to a reduction of diversity in the newly colonized areas. During the Pleistocene, almost the entire current range of the land snail Arianta arbustorum has repeatedly been covered with ice or been subjected to permafrost. Owing to the low potential for dispersal of land snails, slow (re)colonization of the wide range from southern refugia can be excluded. Alternatively, fast, passive dispersal from southern refugia or survival in and expansion from multiple refugia within the area subjected to permafrost may account for the current distribution. To distinguish between these scenarios we reconstructed a phylogeography based on the sequences of a fragment of the cytochrome oxidase I from 133 individuals collected at 45 localities and analysed the molecular variance. Seventy-five haplotypes were found that diverged on average at 7.52% of positions. This high degree of diversity suggests that A. arbustorum is an old species in which the population structure, isolation and the hermaphroditic nature have reduced the probability of lineage extinction. The genetic structure was highly significant with the highest variance partition found among regions. Geographic distance and mitochondrial differentiation were not congruent. Lineages had overlapping ranges. The clear genetic differentiation and the patchy pattern of haplotype distribution suggest that colonization of formerly unsuitable habitats was mainly achieved from multiple populations from within the permafrost area.

Animals↗

PubMed2005

An ancient mitochondrial polymorphism in Adalis bipunctata linked to a sex-ratio-distorting bacterium.

Sex-ratio-distorting microbes are common parasites of arthropods. Although the reasons they have invaded and spread though populations are well understood, their subsequent dynamics within those populations are virtually unknown. We have found that different strains of a male-killing Rickettsia bacterium infecting the beetle Adalia bipunctata are associated with distinct mitochondrial haplotypes, which is expected as both the mitochondria and the bacteria are maternally transmitted. These mitochondrial haplotypes shared a common ancestor >2 million years ago, and their overall diversity is significantly greater than expected under neutrality from comparisons with a nuclear gene. Furthermore, a variety of statistical tests show strong deviations from neutrality in mitochondrial but not in nuclear genes. We therefore conclude that natural selection is probably maintaining a polymorphism of different Rickettsia strains in this species. Despite the age of the different mitochondrial haplotypes, there is very little genetic diversity within them. Furthermore, there is considerable variation in mitochondrial haplotype and bacterial strain frequency between populations, despite it being thought that this species has fairly low levels of population structure. We conclude that the fitness of these male killers may be negatively frequency dependent or different strains may be favored in different populations. These hypotheses await experimental confirmation.

Animals↗

PubMed1992

No evidence for involvement of type 1 collagen structural genes in 'genetic predisposition' to alcoholic cirrhosis.

Type 1 collagen is the predominant collagen in cirrhotic livers. Each type 1 collagen molecule contains three subunits, two are identical (the alpha 1 chains) and the sequence of the third (alpha 2) is very similar. They are encoded at the non-synthenic loci, COL1A1 and COL1A2 and restriction site dimorphisms have been described at each locus. Genetic factors have been invoked as a basis for increased susceptibility to alcoholic cirrhosis. One hypothesis is that genetically determined differences in type 1 collagen may be involved in this predisposition. We have examined this by analysing restriction fragment length polymorphisms at each type 1 collagen locus in leucocyte DNA from 56 unrelated patients with alcoholic cirrhosis and 74 local unrelated healthy controls. Based on the presence or absence of these restriction site dimorphisms four possible haplotypes were generated at COL1A1 and COL1A2. We found no significant difference in allele frequencies between alcoholic cirrhotics and controls and, unlike a previous small study, we found no particular haplotype of either gene was associated with alcoholic cirrhosis. Our study provides no evidence for involvement of type 1 collagen structural genes in a genetic predisposition to cirrhosis in alcoholics.

Collagen↗

PubMed1996

Haplotype and interspersion analysis of the FMR1 CGG repeat identifies two different mutational pathways for the origin of the fragile X syndrome.

To understand the origins of the fragile X syndrome and factors predisposing alleles to instability and hyperexpansion, we have compared the haplotype (using markers FRAXAC1, FRAXAC2, and DXS548) and AGG interspersion patterns of the FMR1 CGG repeat for 214 normal and 16 premutation chromosomes. Association testing between interspersion pattern and haplotype reveals a highly significant (P < 0.002) non-random distribution, indicating that all three markers are useful in phylogenetic reconstruction of mutational change. Parsimony analysis of the FMR1 CGG repeat substructure predicts that loss of AGG interruptions has occurred independently on many haplotypes associated with the fragile X syndrome, partially explaining the haplotype diversity of this disease. Among haplotypes found in linkage disequilibrium with the fragile X mutation, two different modes of mutation and predisposition to instability have been identified. One pathway has involved the frequent and recurrent loss of AGG interruptions from rare asymmetrical ancestral array structures. Intergenerational transmission studies suggest that these predisposed chromosomes progress relatively rapidly to the disease state. In contrast, the second mutational pathway involves a single haplotype which has maintained two AGG interruptions. Parsimony analysis of CGG repeat substructure within this haplotype suggests that larger alleles have been generated by gradual increments of CGG repeats distal to the most 3' interruption. Pedigree analysis of the intergenerational stability of alleles of this haplotype confirms a gradual progression toward instability thresholds. As a result, a large reservoir of chromosomes carrying large repeats on this haplotype exists. These chromosomes are predisposed to disease. The present data support a model in which there are at least two different mutational pathways predisposing alleles to instability and hyperexpansion associated with the fragile X syndrome.

Alleles↗

PubMedDate not supplied

Eurasian otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian Peninsula to Scandinavia.

The Eurasian otter, Lutra lutra, has a Palaearctic distribution and has suffered a severe decline throughout Europe during the last century. Previous studies in this and other mustelids have shown reduced levels of variability in mitochondrial DNA, although otter phylogeographic studies were restricted to central-western Europe. In this work we have sequenced 361 bp of the mtDNA control region in 73 individuals from eight countries and added our results to eight sequences available from GenBank and the literature. The range of distribution has been expanded in relation to previous works north towards Scandinavia, east to Russia and Belarus, and south to the Iberian Peninsula. We found a single dominant haplotype in 91.78% of the samples, and six more haplotypes deviating a maximum of two mutations from the dominant haplotype restricted to a single country. Variability was extremely low in western Europe but higher in eastern countries. This, together with the lack of phylogeographical structuring, supports the postglacial recolonization of Europe from a single refugium. The Eurasian otter mtDNA control region has a 220-bp variable minisatellite in Domain III that we sequenced in 29 otters. We found a total of 19 minisatellite haplotypes, but they showed no phylogenetic information.

Animals↗

PubMed2006

Worldwide phylogeography of the blacktip shark (Carcharhinus limbatus) inferred from mitochondrial DNA reveals isolation of western Atlantic populations coupled with recent Pacific dispersal.

Although many coastal shark species have widespread distributions, the genetic relatedness of worldwide populations has been examined for few species. The blacktip shark, (Carcharhinus limbatus), inhabits tropical and subtropical coastal waters throughout the world. In this study, we examined the genetic relationships of blacktip shark populations (n = 364 sharks) throughout the majority of the species' range using the entire mitochondrial control region (1067-1070 nucleotides). Two geographically distinct maternal lineages (western Atlantic, Gulf of Mexico, and Caribbean Sea clades, and eastern Atlantic, Indian, and Pacific Ocean clades) were identified and shallow population structure was detected throughout their geographic ranges. These findings indicate that a major population subdivision exists across the Atlantic Ocean, but not the Pacific Ocean. The historical dispersal of this widespread, coastal species may have been interrupted by the rise of the Isthmus of Panama. This scenario implies historical dispersal across the Pacific Ocean (supported by the recovery of the same common haplotype from the Philippines, Hawaii, and the Gulf of California reflecting recent/contemporary dispersal abilities) and an oceanic barrier to recent migration across the Atlantic. Genetic structure within the eastern Atlantic/Indo-Pacific (Phi(ST) = 0.612, P < 0.001) supports maternal philopatry throughout this area, expanding previous western Atlantic findings. Eastern Atlantic/Indo-Pacific C. limbatus control region haplotypes were paraphyletic to Carcharhinus tilstoni haplotypes in our maximum-parsimony analysis. The greater divergence of western Atlantic C. limbatus than C. tilstoni from eastern Atlantic/Indo-Pacific C. limbatus reflects the taxonomic uncertainty of western Atlantic C. limbatus.

Animal Migration↗

PubMed2001

Structural and functional imaging with carbon nanotube AFM probes.

Atomic force microscopy (AFM) has great potential as a tool for structural biology, a field in which there is increasing demand to characterize larger and more complex biomolecular systems. However, the poorly characterized silicon and silicon nitride probe tips currently employed in AFM limit its biological applications. Carbon nanotubes represent ideal AFM tip materials due to their small diameter, high aspect ratio, large Young's modulus, mechanical robustness, well-defined structure, and unique chemical properties. Nanotube probes were first fabricated by manual assembly, but more recent methods based on chemical vapor deposition provide higher resolution probes and are geared towards mass production, including recent developments that enable quantitative preparation of individual single-walled carbon nanotube tips [J. Phys. Chem. B 105 (2001) 743]. The high-resolution imaging capabilities of these nanotube AFM probes have been demonstrated on gold nanoparticles and well-characterized biomolecules such as IgG and GroES. Using the nanotube probes, new biological structures have been investigated in the areas of amyloid-beta protein aggregation and chromatin remodeling, and new biotechnologies have been developed such as AFM-based haplotyping. In addition to measuring topography, chemically functionalized AFM probes can measure the spatial arrangement of chemical functional groups in a sample. However, standard silicon and silicon nitride tips, once functionalized, do not yield sufficient resolution to allow combined structural and functional imaging of biomolecules. The unique end-group chemistry of carbon nanotubes, which can be arbitrarily modified by established chemical methods, has been exploited for chemical force microscopy, allowing single-molecule measurements with well-defined functionalized tips.

Animals↗

PubMed1980

Aberrant Ae (E beta) Ia polypeptide chain in H-2g2 haplotype mice. Possible result of an intragenic recombination or mutation.

Mice of strains D2.GD and B10.GD, which carry the recombinant haplotype H-2g2 (previously typed as H-2Kd I-Ad / I-Bb I-Jb I-Eb I-Cb Sb H-2Db), have an Ae (E beta) polypeptide chain electrophoretically distinct from the Ae chains of both b and d haplotype mice, including the progenitor strains from which the recombinant H-2g2 chromosome was derived. The evidence presented suggests that the altered molecular properties of the Aeg2 chain may be a consequence of an intragenic recombination event in the I-A subregion within the structural gene for this polypeptide chain. Because the A alpha and A beta chains controlled by H-2g2 appear to be d haplotype in origin, this finding would map the gene for Ae to the right of the loci controlling the A alpha and A beta chains

Animals↗

PubMed1997

Major histocompatibility complex (MHC) class III genetics in two Amerindian tribes from southern Brazil: the Kaingang and the Guarani.

Population genetic studies of the major histocompatibility complex (MHC) class III region, comprising C2, BF and C4 phenotypes, and molecular genetic data are rarely available for populations other than Caucasoids. We have investigated three Amerindian populations from Southern Brazil: 131 Kaingang from Ivaí (KIV), 111 Kaingang (KRC) and 100 Guarani (GRC) from Rio das Cobras. Extended MHC haplotypes were derived after standard C2, BF, C4 phenotyping and restriction fragment length polymorphism (RFLP) analysis with TaqI, together with HLA data published previously by segregation analysis. C2 and BF frequencies corresponded to other Amerindian populations. C4B*Q0 frequency was high in the GRC (0.429) but low in the Kaingang. Unusual C4 alleles were found, viz. C4A*58, A*55 and C4B*22 (presumably non-Amerindian) and aberrant C4A*3 of Amerindian origin occurring with a frequency of 0.223 in the GRC. C4A*3 bands of homo- and heterozygous individuals carrying this variant were Rodgers 1 positive and Chido 1,3 positive, showed a C4A specific lysis type and a C4A like alpha-chain. Polymerase chain reaction studies and sequencing showed that this is based on a C4A*3 duplication with a regular C4A*3 and a partially converted C4A*0304 carrying the C4B specific epitopes Ch 6 and Ch 1,3. Associations of class III haplotypes with particular RFLP patterns were similar to those reported for Caucasoids. The previously described association between combined C4A and CYP21P deletions and the 6.4 kb TaqI fragment was not seen in these Amerindians. This fragment occurred within a regular two locus gene structure in the Kaingang, representing a "short" gene at C4 locus I. C4 and CYP21 duplications were frequently observed. The distribution of extended MHC haplotypes provides evidence for a close relationship between the KIV and KRC and a larger genetic distance between the two Kaingang groups and the GRC.

Brazil↗

PubMed2001

Comparative single-strand conformation polymorphism (SSCP) and microscopy-based analysis of nitrogen cultivation interactive effects on the fungal community of a semiarid steppe soil.

The effects of nitrogen accretion on fungal diversity and community structure in early-seral (cultivated) and native (uncultivated) shortgrass steppe soils were evaluated using single-strand conformation polymorphism (SSCP) and microscopy in a comparative experiment. Selected haplotypes generated from fungal 18S gene fragments were also sequenced for species identification. Microscopy-based analyses showed significantly shorter fungal hyphal lengths in the early-seral control plots in comparison with the native control plots (P<0.0003), independent of nitrogen addition. Although diversity indices did not show significant differences between the plots, SSCP analyses indicated that fungal community structure differed in the native and early-seral control sites. In nitrogen-amended sites, gene sequences from dominant haplotypes indicated a shift to a more common nitrogen-impacted fungal community. While nitrogen amendments appear to be more important than cultivation in influencing these soil fungal communities, hyphal lengths were only decreased due to cultivation. The use of microscopic and molecular techniques, as carried out in this study, provided integrative information concerning fungal community responses to wide spread stresses being imposed globally on terrestrial ecosystems, that is not provided by the individual techniques.

Journal Article↗

PubMed1995

[Interrelationship between structural variants of the apolipoprotein B and ischemic heart disease and plasma lipid levels].

Xba I and EcoR I polymorphism of the apolipoprotein B (APOB) gene was studied by PCR. A significant increase in the frequency of allele X+ and haplotype H+E+ was demonstrated in patients with coronarographically documented coronary heart disease (CHD) over that of the general population. Association of allele E- with increased levels of serum triglycerides was found. The results provide evidence about the contribution of structural variants of the APOB gene to determining CHD.

Adult↗