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PubMed2002

Cryptic lineages in a small frog: the post-glacial history of the spring peeper, Pseudacris crucifer (Anura: Hylidae).

The spring peeper (Pseudacris crucifer) is believed to have been a primary herpetological invader of eastern North America following the most recent period of glacial retreat. We examined the phylogeographic pattern and population structure of P. crucifer to determine whether the distribution of haplotypic variants reflect post-Pleistocene recolonization dynamics. A number of geographically isolated evolutionary lineages were supported by both maximum parsimony and neighbor-joining analyses, and by coalescence approaches applied to mtDNA. South-western Ontario represents a high level of genotypic diversity (pi) due to the presence of two divergent lineages. The geographic distribution of these lineages are interpreted as reflecting post-glacial recolonization dynamics from separate, isolated refugia during the late Pleistocene that have come into secondary contact in SW Ontario. The phylogenetic placement of haplotypes from the range of P. crucifer bartramiana (Florida and South Carolina) does not allow for monophyly of P. crucifer crucifer, and therefore the bartramiana subspecies designation does not reflect a separate evolutionary lineage.

Animals↗

PubMed2006

Development of a method for the genetic identification of mussel species belonging to Mytilus, Perna, Aulacomya, and other genera.

Legislation regarding the labeling of processed products is an important issue in the protection of consumer rights. This labeling is especially important in products that cannot be identified on the basis of their morphological characters, because these are removed from the animal in the transformation process. The goal of this study was the identification of mussel species using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Forensically Informative Nucleotide Sequencing (FINS) methodologies. The molecular marker selected was 18S rDNA (nuclear small-subunit rDNA gene), which allows identification at the genus level and at the species level in some cases. The genera included in this study were Mytilus, Perna, Aulacomya, Semimytilus, Brachidontes, Choromytilus, and Perumytilus. Different markers were used for genetic identification at the species level. To identify the species included in the genus Perna and Choromytilus, a fragment of ITS 1 (Internal Transcribed Spacer 1) was amplified by multiplex PCR and digested with restrictases. The species of Mytilus were identified by length polymorphism and RFLP of the polyphenolic adhesive protein gene. This methodology was validated with products manufactured in the authors' pilot plant and applied to commercial samples. Therefore, this sequential method can be completely or partially used to determine the mussel genus or species present in any food product.

Animals↗

PubMed2006

Estimating sex-specific processes in human populations: Are XY-homologous markers an effective tool?

Homologous markers on the sex-specific regions of the X- and Y-chromosomes are differentially inherited through males and females, and have similar molecular characteristics. They may therefore be useful as a complement to the comparison of mtDNA and Y-chromosomal haplotypes for estimating sex-specific processes shaping human population structure. To test this idea, we analyzed XY-homologous microsatellite diversity in 33 human populations from Africa, Asia and Europe. Interpopulation comparisons suggest that the generally discordant pattern of genetic variation observed for X- and Y-linked markers could be an outcome of sex-specific migration processes (m(females)/m(males) approximately 3) or sex-specific demographic processes (N(females)/N(males) approximately 11) or a combination of both. However, intrapopulation diversity estimated by the X/Y ratio Watterson estimator (theta(H(Y))/theta(H(X))) suggests that the scenarios required to explain the global genetic variation of XY-homologous markers are many and complex, and that the sex-specific processes (effective population size and migration rate) shaping human population structures are likely to be specific to each population under study. XY-homologous markers provide an insight into the genuine complexity of sex-specific processes, and their further exploitation in human population studies seems worthwhile.

Africa↗

PubMed2002

Population genetic structure of Tomicus piniperda L. (Curculionidae: Scolytinae) on different pine species and validation of T. destruens (Woll.).

Genetic diversity and population structure of Tomicus piniperda was assessed using mitochondrial sequences on 16 populations sampled on 6 pine species in France. Amplifications of Internal transcribed space 1 (ITS1) were also performed. Our goals were to determine the taxonomic status of the Mediterranean ecotype T. piniperda destruens, and to test for host plant or geographical isolation effect on population genetic structure. We showed that T. piniperda clusters in two mtDNA haplotypic groups. Clade A corresponds to insects sampled in continental France on Pinus sylvestris, P. pinaster and P. uncinata, whereas clade B gathers the individuals sampled in Corsica on P. pinaster and P. radiata and in continental France on P. pinea and P. halepensis. Insects belonging to clade A and clade B also consistently differ in the length of ITS1. Individuals belonging to both clades were found once in sympatry on P. pinaster. Genetic distances between clades are similar to those measured between distinct species of Tomicus. We concluded that clade B actually corresponds to the destruens ecotype and forms a good species, T. destruens. Analyses of molecular variance ( amova ) were conducted separately on T. destruens and T. piniperda to test for an effect of either geographical isolation or host species. Interestingly, the effect of host plant was significant for T. piniperda only, while the effect of geographical isolation was not. Pine species therefore seems to act as a significant barrier to gene flow, even if host race formation is not observed. These results still need to be confirmed by nuclear markers.

Animals↗

PubMed2001

The S receptor kinase gene determines dominance relationships in stigma expression of self-incompatibility in Brassica.

Self-incompatibility (SI) in Brassica is sporophytically controlled by the multi-allelic S locus. SI phenotypes of the stigma and pollen in an S heterozygote are determined by the two S haplotypes it carries; the two haplotypes may be co-dominant or exhibit a dominant/recessive relationship. Because the S receptor kinase (SRK) gene of the S locus was recently shown to determine the S haplotype specificity of the stigma, we wished to investigate whether SRK also plays a role in the dominance relationships between S haplotypes. We crossed plants carrying an SRK28 transgene with plants homozygous for one of five S haplotypes that are either co-dominant with, or recessive to, S28 haplotype in the stigma, and analyzed the SI phenotypes of the progeny. In all cases, the SI phenotype of the stigma of plants carrying the SRK28 transgene could be predicted by the known dominance relationships between the S haplotype(s) and the S28 haplotype. Moreover, in the S43 homozygote carrying the SRK28 transgene where the S43 phenotype in the stigma was masked by the presence of the SRK28, the transcript level of SRK28 was found to be much lower than that of SRK43. All these results suggest that the dominance relationships between S haplotypes in the stigma are determined by SRK, but not by virtue of its relative expression level.

Blotting, Northern↗

PubMed1993

Susceptibility to rheumatoid arthritis is not associated with a single common allele of the type 2 collagen gene (COL2A1)

Type 2 collagen is quantitatively the most important constituent of articular cartilage which is the target of progressive destruction in RA. Polymorphism of type 2 collagen could theoretically influence the development of RA either by rendering the cartilage matrix particularly susceptible to autoimmune attack or subsequent degradation. We have investigated the possibility that there is a common allele of type 2 collagen associated with RA by analysing a dimorphism of the corresponding structural gene (COL2A1) in healthy and diseased individuals. We compared haplotype frequencies, defined by the presence or absence of a Hind III restriction site at the COL2A1 locus (encoding type 2 collagen), in 98 patients with classical/definite RA and 158 controls. No differences were seen between the frequencies of individual genotypes in the two groups (maximum chi 2 = 0.7), indicating that susceptibility to this disease does not appear to be determined by the presence of a single common allelic variant at this locus.

Alleles↗

PubMed1999

Ridges and rivers: a test of competing hypotheses of Amazonian diversification using a dart-poison frog (Epipedobates femoralis).

Mitochondrial DNA cytochrome b sequence data from a dart-poison frog, Epipedobates femoralis, were used to test two hypotheses of Amazonian diversification: the riverine barrier and the ridge hypotheses. Samples were derived from sites located on both banks of the Rio Juruá and on both sides of the Iquitos Arch in western Amazonia. The phylogeographic structure was inconsistent with predictions of the riverine barrier hypothesis. Haplotypes from opposite river banks did not form monophyletic clades in any of our phylogenetic analyses, nor was the topology within major clades consistent with the riverine hypothesis. Further, the greatest differentiation between paired sites on opposite banks was not at the river mouth where the strongest barrier to gene flow was predicted to occur. The results instead were consistent with the hypothesis that ancient ridges (arches), no longer evident on the landscape, have shaped the phylogeographic relationships of Amazonian taxa. Two robustly supported clades map onto opposite sides of the Iquitos Arch. The mean haplotypic divergence between the two clades, in excess of 12%, suggests that this cladogenic event dates to between five and 15 million years ago. These estimates span a period of major orogenesis in western South America and presumably the formation of these ancient ridges.

Animals↗

PubMed2006

The portability of tagSNPs across populations: a worldwide survey.

In the search for common genetic variants that contribute to prevalent human diseases, patterns of linkage disequilibrium (LD) among linked markers should be considered when selecting SNPs. Genotyping efficiency can be increased by choosing tagging SNPs (tagSNPs) in LD with other SNPs. However, it remains to be seen whether tagSNPs defined in one population efficiently capture LD in other populations; that is, how portable tagSNPs are. Indeed, tagSNP portability is a challenge for the applicability of HapMap results. We analyzed 144 SNPs in a 1-Mb region of chromosome 22 in 1055 individuals from 38 worldwide populations, classified into seven continental groups. We measured tagSNP portability by choosing three reference populations (to approximate the three HapMap populations), defining tagSNPs, and applying them to other populations independently on the availability of information on the tagSNPs in the compared population. We found that tagSNPs are highly informative in other populations within each continental group. Moreover, tagSNPs defined in Europeans are often efficient for Middle Eastern and Central/South Asian populations. TagSNPs defined in the three reference populations are also efficient for more distant and differentiated populations (Oceania, Americas), in which the impact of their special demographic history on the genetic structure does not interfere with successfully detecting the most common haplotype variation. This high degree of portability lends promise to the search for disease association in different populations, once tagSNPs are defined in a few reference populations like those analyzed in the HapMap initiative.

Chromosomes, Human, Pair 22↗

PubMed1998

Mapping of the T-cell epitope in the major 43-kilodalton glycoprotein of Paracoccidioides brasiliensis which induces a Th-1 response protective against fungal infection in BALB/c mice.

The 43-kDa glycoprotein of Paracoccidioides brasiliensis is the major diagnostic antigen of paracoccidioidomycosis, the prevalent systemic mycosis of Latin America. Apart from eliciting high antibody titers, gp43 is also immunodominant in delayed-type hypersensitivity reactions in infected animals and humans. The cellular immune response in mice to gp43 administered in complete Freund's adjuvant involves CD4+ Th-1 lymphocytes, secreting gamma interferon (IFN-gamma) and interleukin 2 (IL-2) but not IL-4 and IL-10. The T-cell epitope of this antigen was mapped to a 15-amino-acid peptide (P10) based on lymphoproliferations with primed cells from three different haplotypes and on a computer-assisted protein analysis. The structural requirements of the T-cell epitope were determined by assaying a series of P10 analogous and truncated peptides. Only 12-mer or longer sequences were active, confirming presentation by major histocompatibility complex II. The HTLAIR inner core of P10 is the essential domain of the epitope, with various flanking regions possible. Immunization of mice with both gp43 and P10 led to vigorous protection against intratracheal challenge by virulent P. brasiliensis, with a >200-fold decrease in lung CFU and halting of dissemination to the spleen and liver. The protective effect of P10 is mainly attributed to an IFN-gamma-mediated cellular immune response. Unlike gp43, which induces an antibody response compatible with both Th-1 and Th-2 activation in infected BALB/c mice, P10 does not induce a humoral response. Protection by gp43 and P10 was characterized by a few well-demarcated lung granulomas with numerous nonviable yeast forms or resolved lesions with no detectable fungal cells.

Animals↗

PubMed2006

The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like Loci.

The innate and adaptive immune systems of vertebrates possess complementary, but intertwined functions within immune responses. Receptors of the mammalian innate immune system play an essential role in the detection of infected or transformed cells and are vital for the initiation and regulation of a full adaptive immune response. The genes for several of these receptors are clustered within the leukocyte receptor complex (LRC). The purpose of this study was to carry out a detailed analysis of the chicken (Gallus gallus domesticus) LRC. Bacterial artificial chromosomes containing genes related to mammalian leukocyte immunoglobulin-like receptors were identified in a chicken genomic library and shown to map to a single microchromosome. Sequencing revealed 103 chicken immunoglobulin-like receptor (CHIR) loci (22 inhibitory, 25 activating, 15 bifunctional, and 41 pseudogenes). A very complex splicing pattern was found using transcript analyses and seven hypervariable regions were detected in the external CHIR domains. Phylogenetic and genomic analysis showed that CHIR genes evolved mainly by block duplications from an ancestral inhibitory receptor locus, with transformation into activating receptors occurring more than once. Evolutionary selection pressure has led not only to an exceptional expansion of the CHIR cluster but also to a dramatic diversification of CHIR loci and haplotypes. This indicates that CHIRs have the potential to complement the adaptive immune system in fighting pathogens.

Alternative Splicing↗

PubMed1992

Population structure and mitochondrial DNA gene flow in Old World populations of Drosophila subobscura.

An extensive survey of mitochondrial DNA (mtDNA) restriction polymorphism in 156 isofemale lines from 29 different geographic populations of Drosophila subobscura distributed throughout the Old World was carried out. Ten restriction enzymes were used, five of which revealed restriction site polymorphism. Of the 31 restriction sites detected, 13 were found to be polymorphic. Comparisons with the mtDNA map of Drosophila yakuba indicate that the variable sites are mainly concentrated in protein genes, especially those corresponding to the NADH complex. A total of 13 different haplotypes were observed, two of which (haplotypes I and II) are quite frequent and widely distributed throughout the populations, whereas the other 11 with the exception of VIII, which deserves special attention, are each restricted to one population only and occur at low frequencies. The observed distribution of haplotypes, corroborated by a parsimonious unrooted tree, suggests an ancient origin of haplotypes I and II in the continent. In order to compare genetic structure according to mtDNA and allozymes, the 10 populations with higher population sizes were studied for 10 polymorphic allozymes also. One striking result is the high degree of population structure of the mtDNA when compared to that obtained for allozymes. If an island model is assumed, estimates of gene flow give values of 0.013 and 1.89 migrants per generation for mtDNA and allozymes, respectively. What is apparent from these estimates is that Drosophila subobscura populations are effectively subdivided for mtDNA genes at migration rates at which nuclear genes (allozymes) are almost panmictic.

Alleles↗

PubMed2005

The hypervariable domain of the mitochondrial control region in Atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring.

Atlantic spiny lobsters support major fisheries in northeastern Brazilian waters and in the Caribbean Sea. To avoid reduction in diversity and elimination of distinct stocks, understanding their population dynamics, including structuring of populations and genetic diversity, is critical. We here explore the potential of using the hypervariable domain in the control region of the mitochondrial DNA as a genetic marker to characterize population subdivision in spiny lobsters, using Panulirus argus as the species model. The primers designed on the neighboring conserved genes have amplified the entire control region (approx. 780 bases) of P. argus and other closely related species. Average nucleotide and haplotype diversity within P. argus were found to be high, and population structuring was hypothesized. The data suggest a division of P. argus into genetically different phylogeographic groups. The hypervariable domain seems to be useful for determining genetic differentiation of geographically distinct stocks of P. argus and other Atlantic spiny lobsters.

Animals↗

PubMed2000

Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.

The Duffy blood group locus, which encodes a chemokine receptor, is characterized by three alleles-FY*A, FY*B, and FY*O. The frequency of the FY*O allele, which corresponds to the absence of Fy antigen on red blood cells, is at or near fixation in most sub-Saharan African populations but is very rare outside Africa. The FST value for the FY*O allele is the highest observed for any allele in humans, providing strong evidence for the action of natural selection at this locus. Homozygosity for the FY*O allele confers complete resistance to vivax malaria, suggesting that this allele has been the target of selection by Plasmodium vivax or some other infectious agent. To characterize the signature of directional selection at this locus, we surveyed DNA sequence variation, both in a 1.9-kb region centered on the FY*O mutation site and in a 1-kb region 5-6 kb away from it, in 17 Italians and in a total of 24 individuals from five sub-Saharan African populations. The level of variation across both regions is two- to threefold lower in the Africans than in the Italians. As a result, the pooled African sample shows a significant departure from the neutral expectation for the number of segregating sites, whereas the Italian sample does not. The FY*O allele occurs on two major haplotypes in three of the five African populations. This finding could be due to recombination, recurrent mutation, population structure, and/or mutation accumulation and drift. Although we are unable to distinguish among these alternative hypotheses, it is likely that the two major haplotypes originated prior to selection on the FY*O mutation.

Africa South of the Sahara↗

PubMed2003

Cytotoxic T-cell activity is not detectable in Venezuelan equine encephalitis virus-infected mice.

Previously published research has established that the immune response to the Venezuelan equine encephalitis virus (VEEV) vaccine strain TC-83 is Th 1-mediated, with local activation of both CD4+ and CD8+ T cells. This suggests that cytotoxic lymphocytes CTL may play a role in protection against virulent VEEV. Studies involving a variety of immunisation schedules with either TC-83 or strain CAAR 508 (serogroup 5) of VEEV, and six different haplotypes of mice, failed to reveal functional CTL activity against VEEV-infected targets in secondary antigen-stimulated lymphocyte cultures from either the draining lymph nodes (LN) or spleen. Nor were VEEV-specific CTL detected after immunisation of mice (three haplotypes) with recombinant vaccinia viruses (VV) expressing either the non-structural (nsP1-4) or the structural (C-E3-E2-6K-E1) genes of TC-83. Reciprocal experiments in which mice were immunised with TC-83, and their lymphocytes tested against VV recombinant-infected targets also failed to detect CTL activity. These data suggest that VEEV infection of mice does not elicit detectable CTL activity, and that CTL are unlikely to play a role in protection against virulent VEEV.

Animals↗

PubMed2000

Glacial refugia of limber pine (Pinus flexilis James) inferred from the population structure of mitochondrial DNA.

To make inferences about the glacial refugia that harboured the limber pine, Pinus flexilis James, we examined the range-wide population structure of mitochondrial DNA (mtDNA) with eight size variants in the second intron of nad1. The data consisted of haplotypes from 704 trees collected from 40 localities. The value of FST for these populations was 0.80, which is a much larger value than has been reported for allozymes and chloroplast DNA (cpDNA) in limber pine, and it suggests that the number of seeds moving among localities per generation is approximately 0.12. Gene flow of this magnitude would allow mutation and subsequent genetic drift to have a substantial impact on the population structure of mtDNA. The majority of the mtDNA haplotypes are restricted to minor portions of the geographical range. The data are consistent with mtDNA differentiation in seven glacial refugia, followed by dispersal out of those refugia.

Alberta↗

PubMed2006

[Analysis of polymorphisms in Y-DNA haplotypes and mtDNA haplogroups in Yao ethnic group from Guizho].

The frequencies of Y-chromosome haplotypes consisting of 12 single nucleotide polymorphisms (SNP) and mitochondrial DNA (mtDNA) haplotypes consisting of 9 SNPs were investigated using PCR-RFLP in 97 Yaos from Guizhou to study the patrilineal and matrilineal genetic structure and the origin of Yao Ethnic Group from Guizhou. Results showed that all 97 samples were classified into 4 Y-DNA haplotypes (H7, H8, H9 and H11). The major haplotype H7 of Hmong-Mien Population was highly prevalent (92.4%) in Yaos from Guizhou. Eight mtDNA haplotypes were identified through mtDNA analysis and all the haplotypes could be classified into 5 haplogroups (B4, B5, D4, D5 and N*) that were defined previously. The frequency of a 9-bp deletion in the human mtDNA Co II/tRNALys intergenic region was 58.2% in the 97 samples. These data suggest that the patrilineal genetic structure of Yao ethnic group from Guizhou was simple and Yaos from Guizhou had the typical genetic character of the Hmong-Mien Population and some admixture with other populations. The matrilineal genetic structure of Yaos from Guizhou was relatively complex and the 9-bp deletion was a characteristic genetic marker of the matrilineal genetic structure of Yaos from Guizhou.

Asian People↗

PubMed2005

Klotho gene polymorphisms are associated with osteocalcin levels but not bone density of aged postmenopausal women.

Osteoporosis is known to have a strong genetic basis. It has been proposed that polymorphisms within the KL (klotho) gene have a significant effect on aging, in particular, the osteoblast defect of aging. The association between polymorphisms within this gene and biochemical markers of bone formation and resorption, bone structure, and fracture rates was studied in 1,190 postmenopausal women with a mean age of 75 years. Genotyping of these polymorphic sites was carried out using Matrix-Assisted Laser Desorption Ionization--Time of Flight (MALDI-ToF) mass spectrometry. The G allele of SNP c.1775G>A was associated with a lower osteocalcin level than the A allele (P = 0.004) in a codominant model. SNPs C-387T and IVS1+8262c>t both showed nonsignificant associations with osteocalcin (P values of 0.063 and 0.068, respectively), but a haplotype analysis of 2 of 5 haplotypes of the three SNPs with a frequency greater than 4% revealed a significant association with osteocalcin (P = 0.036). None of the individual polymorphisms or haplotypes analyzed showed any associations with a marker of bone resorption the deoxypyridinoline creatinine ratio, bone structure, or fracture data. Therefore, the G polymorphism within the c.1775G>A SNP site and a haplotype including this are associated with a reduced osteoblast product osteocalcin. These data suggest that variation in the KL gene product affects osteoblast activity independent of osteoclast activity but that this defect does not result in an effect on bone structure in this population, perhaps because of "rescue" by other genetic or environmental factors in this population.

Absorptiometry, Photon↗

PubMed2005

[The sequence polymorphism of Y-chromosome DNA and mtDNA of Dong Ethnic of Congjiang, Guizhou].

To study the patrilineal and matrilineal genetic structure and the origin of Dong Ethnic of Congjiang Guizhou. Study the distribution of Y-chromosome haplotypes which consisted of 10 SNPs of Y-DNA and mtDNA haplogroups consisted of 11 SNPs by using PCR-RFLP method. The result is three haplotypes H6,H11,H14 were detected, the frequency of H11 is 92.5%. Six haplogroups were identified by mtDNA analysis, 75% of the people can be identified. The patrilineal genetic structure of Dong of Guizhou is simple, Principle component indicated that the structure is closer to Zhuang-Dong branch of Sino-Tibetan language family. The matrilineal genetic structure of Dong of Guizhou is complicated.

Asian People↗