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PubMed1996

Mitochondrial DNA sequence variation and phylogeography of Pimelia darkling beetles on the island of Tenerife (Canary Islands).

Four morphological taxa of the beetle genus Pimelia (Coleoptera, Tenebrionidae) are known to exist on the Atlantic island of Tenerife. We have obtained DNA sequences for 61 individuals from these taxa across the island for a 200 bp long fragment of the mitochondrial COI gene. In addition, a restriction site polymorphism in the nuclear rRNA ITS-1 sequence was identified and screened in a sample of these individuals using the enzyme Kpn2I. The results were analysed using approaches which allow inferences to be made about the population genetic structure and the mitochondrial genealogy of these closely related beetles. The mtDNA haplotype distribution and the estimates of sequence divergence revealed the presence of two ancient mtDNA lineages which coincide with the disjunct volcanic evolution of the island. The ITS-1 polymorphism was found to be diagnostic of these two lineages. However, the morphological and mitochondrial phylogenies were found to be discordant. We argue that this is possibly the result of rapid morphological change, produced by selection in different habitats, which has been recently superimposed on an older mitochondrial DNA divergence.

Animals↗

PubMed1997

NCAM and schizophrenia: genetic studies.

The hypothesis of a neurodevelopmental dysfunction being involved in the etiology of schizophrenia is suggested by the observation of morphological alterations in the brains of schizophrenia patients. These alterations may be caused by defects in neural cell differentiation or migration, which could lead to disrupted neuronal circuitry and to the schizophrenia symptomatology. The neural cell adhesion molecule (NCAM) plays a major role in cell migration and axon outgrowth, and is involved in synaptic plasticity mechanisms implicated in adult cognitive functions. Altered levels of the NCAM polysialylated form, PSA-NCAM, in the brain of schizophrenia patients have been reported, and are supportive of a role for this molecule in the disorder. To investigate the possible involvement of the NCAM gene in schizophrenia, we conducted a comprehensive genetic study, which included linkage analysis and an association study employing the Haplotype Relative Risk (HRR) design in nuclear families. Our results indicate that structural alterations in the NCAM gene are unlikely to play a major role in schizophrenia, although a function for the NCAM molecule in the etiology of the disease remains an intriguing hypothesis.

Adult↗

PubMed2004

Genetic diversity patterns in the SR-BI/II locus can be explained by a recent selective sweep.

The human scavenger receptor class B type I (SR-BI and splice variant SR-BII) plays a central role in HDL cholesterol metabolism and represents a candidate gene for a number of related diseases. We examined the genetic diversity of its coding and flanking regions in a sample of 178 chromosomes from individuals of European, African, East Asian (including Southeast Asian), Middle-Eastern as well as Amerindian descent. Nine of the 14 polymorphisms observed are new. Four of the five variants causing amino acid replacements, G2S, S229G, R484W, and G499R, are likely to affect protein structure and function. SR-BI/BII diversity is partitioned among 19 haplotypes; all but one interconnected by single mutation or a recombination event. Such tight haplotype network and the unusual geographic partitioning of this diversity, high not only in Africa but in East Asia as well, suggests its recent origin and possible effect of selection. Coalescent analysis infers a relatively short time to the most recent common ancestor and points to population expansion in Africa and East Asia. These two continents differ significantly in pairwise F(ST) values, differing as well from a single cluster formed by Europe, Middle East and America. In the context of findings for similarly analyzed other loci, we propose that a selective sweep at the origin of modern human populations could explain the low level of ancestral SR-BI/II diversity. The unusually deep split between Africa and Asia, well beyond the Upper Paleolithic when inferred under neutrality, is consistent with subsequent geographical and demographic expansion favoring the accumulation of new variants, especially in groups characterized by large effective population sizes, such as Asians and Africans. The relevance of such partitioning of SR-BI/II diversity remains to be investigated in genetic epidemiological studies which can be guided by the present findings.

CD36 Antigens↗

PubMed2004

Testing the out-of-Florida hypothesis on the origin of cheating in the yucca-yucca moth mutualism.

Mutualistic interactions can be exploited by cheaters that take the rewards offered by mutualists without providing services in return. The evolution of cheater species from mutualist ancestors is thought to be possible under particular ecological conditions. Here we provide a test of the first explicit model of the transition from mutualism to antagonism. We used the obligate pollination mutualism between yuccas and yucca moths to examine the origins of a nonpollinating cheater moth, Tegeticula intermedia, and its pollinating sister species, T. cassandra. Based on geographic distribution and ecological factors affecting the pollinators, previous research had indicated that the cheaters evolved in Florida as a result of sympatry of T. cassandra and another pollinator species. We used mitochondrial DNA (mtDNA) sequences and amplified fragment length polymorphism (AFLP) data to investigate the phylogeographic history of the pollinator-cheater sister pair and to test whether the cheaters arose in Florida. Contrary to predictions, phylogenetic and population genetic analyses suggested that the cheaters evolved in the western United States and subsequently spread eastward. Western populations of cheaters had the most ancestral haplotypes and the highest genetic diversity, and there was also significant genetic structure associated with a geographic split between eastern and western populations. In comparison, there was evidence for weak genetic structure between northern and southern pollinator populations, suggesting a long history in Florida. The western origin of the cheaters indicated that the pollinators have more recently become restricted to the southeastern United States. This was supported by AFLP analyses that indicated that the pollinators were more closely related to the western cheaters than they were to geographically proximate cheaters in the east. Shared mtDNA between pollinators and eastern cheaters suggested hybridization, possibly in a secondary contact zone. The results negate the out-of-Florida hypothesis and reveal instead a long, complex, and disparate history for the pollinator-cheater sister pair.

Animals↗

PubMed2006

Evolutionary history of Salmonella typhi.

For microbial pathogens, phylogeographic differentiation seems to be relatively common. However, the neutral population structure of Salmonella enterica serovar Typhi reflects the continued existence of ubiquitous haplotypes over millennia. In contrast, clinical use of fluoroquinolones has yielded at least 15 independent gyrA mutations within a decade and stimulated clonal expansion of haplotype H58 in Asia and Africa. Yet, antibiotic-sensitive strains and haplotypes other than H58 still persist despite selection for antibiotic resistance. Neutral evolution in Typhi appears to reflect the asymptomatic carrier state, and adaptive evolution depends on the rapid transmission of phenotypic changes through acute infections.

Adaptation, Physiological↗

PubMed2000

X-linked vacuolar myopathies: two separate loci and refined genetic mapping.

X-linked vacuolar myopathies can be divided into two forms: one that is associated with cardiomyopathy and mental retardation (XVCM-MR) and a second form, termed X-linked myopathy with excessive autophagy (XMEA), that spares cardiac muscle and has no central nervous system involvement. In this article, we demonstrate linkage between XMEA and markers on chromosome Xq28 and assign the XMEA gene locus to the most telomeric 10.5 cM of chromosome X. We also show that XVCM-MR is not allelic to XMEA.

Adolescent↗

PubMed1989

[An experimental study of spontaneously diabetic Bio Breeding/Worcester (BB/W) rats--with special references to the rat MHC (RT1) in the development of the disease].

The role of rat MHC (RT1) in the development of diabetes mellitus was studied on the Bio Breeding/Worcester (BB/W) rat, an experimental model animal for human juvenile onset (Insulin-dependent, Type 1) diabetes mellitus. The rate of the development of diabetes mellitus was as follows; 35/45 (77.8%) in inbred BB/W rats (u/u haplotype), and 5/397 (1.7%) in F2 rats. Histopathological examinations demonstrated that there were lymphocytic thyroiditis, T cell depletion in the spleen and in the lymph nodes, and extramedullary hematopoiesis, in addition to typical lymphocytic insulitis in the pancreas. Immunohistochemically, the expression of class II antigens in the pancreas was shown to be highly concerned with the histopathological changes and the clinical onset of the diabetes mellitus. Analysis of subsets of infiltrating cells demonstrated that macrophages appeared in the pancreas prior to the onset of the disease. And it was suggested that the infiltrated OX 6+ macrophages functioned as antigen presenting cells, leading to expression of the class II antigens on the surface of islet cells, and finally caused severe lymphocytic insulitis. However, BB/W rats showed complete negative immunohistochemical stainings with a monoclonal antibody HOK 2B, which stained other rat strains carrying RT1u class II antigen (TO, SDJ). Moreover, differences in blocking effect of HOK 2B were found on mixed lymphocyte reactions (MLR) between BB/W and other strains with RT1u haplotype. These findings raise the possibility that minor heterogeneities exist in the structure of class II molecules in RT1u rats including BB/W, which might be closely related to the onset of the disease.

Animals↗

PubMed1984

Cell-mediated cytotoxicity against allogeneic mutant H-2 antigens: restricted and nonrestricted responses.

Two "gain and loss" type mutations of the H-2D region, the H- 2bm13 and H- 2bm14 , resulted in the expression of noncross-reactive CML determinants that are unique to each mutation, the Dbm13 gains and Dbm14 gains, respectively. According to the results of direct cytolytic and competitive inhibition assays of in vitro induced primary cytotoxic T lymphocytes, allogeneic responses specific for Dbm13 gains are generated by responders bearing the H-2b ( KbIbDb ) haplotype, but not by responders bearing the H- 2bm14 ( KbIbDbm14 ), KbIbDd , KbIbDk , or KbIb / qDq haplotype. Responses by the non-H-2b responders against Dbm13 are limited to those determinants shared by the Dbm13 and Db molecules. Because congenic mice differing only at the H-2D region are either responsive or nonresponsive to Dbm13 gains, the responsiveness is controlled by gene(s) in the H-2D region. F1 hybrid offspring of responsive (H-2b) and nonresponsive (non-H-2b) parents are invariably responsive, indicating genetic dominance of the responsiveness. In contrast to the response against Dbm13 gains, cytotoxicity specific for Dbm14 gains is generated by responders bearing the H-2b, H- 2bm13 , KbIbDd , KbIbDk , or KbIb / qDq haplotype. These data indicate the existence of two types of allogeneic MHC determinants; one, represented by Dbm14 gains, is the classic type capable of eliciting CML responses in mice of a wide range of H-2 haplotypes, whereas the other, exemplified by Dbm13 gains, elicits CTL responses only in mice of a few related haplotypes. It is proposed that recognition of Dbm13 gains is restricted by structures shared by Db and Dbm13 but missing from other D (or L, R, etc.) molecules, such as Dbm14 , Dd, Dk, and Dq. Availability of various restricting structures in self MHC molecules may thus influence the alloreactive CTL repertoire.

Animals↗

PubMed1980

A "nonidiotypic" inhibition of influenza-immune H-2-restricted CTL by an anti-T cell serum.

A xenogeneic serum directed at alloimmune CTL is shown to block H-2-restricted anti-viral CTL activity. Extensive absorption studies with targets and effector cells indicate that the blocking is at the level of the CTL and not the target cells. Inhibition is demonstrated for influenza-specific cytotoxicity operating in the context of 3 distinct H-2 haplotypes, suggesting that the serum is not directed at antigen-recognition structures. Kinetic studies on the addition of RAT to an ongoing 51Cr release assay further support the hypothesis that inhibition is not operating via the idiotypic region of the antigen receptor. We suggest that RAT is specific for CTL surface structures involved in nonrecognition events--possibly the lytic sites or a conserved region (idiotype-negative) of th antigen-binding receptor.

Animals↗

PubMed1987

Ia-restricted B-B cell interaction. I. The MHC haplotype of bone marrow cells present during B cell ontogeny dictates the self-recognition specificity of B cells in the polyclonal B cell activation by a B cell differentiation factor, B151-TRF2.

We have demonstrated that B cell recognition of Ia molecules is involved in polyclonal B cell differentiation by B151-TRF2. The present study was undertaken to examine the Ia recognition specificity of B151-TRF2-responsive B cells in fully major histocompatibility complex (MHC)-allogeneic P1----P2, semiallogeneic P1----(P1 x P2)F1, and double donor (P1 + P2)----(P1 x P2)F1 and (P1 + P2)----P1 radiation bone marrow chimeras. The B cells from both P1----P2 and P1----(P1 x P2)F1 chimeras could give rise to in vitro immunoglobulin M-producing cells upon stimulation with B151-TRF2 comparable in magnitude to that of normal P1 B cells, and their responses were inhibited by anti-I-AP1 but not by anti-I-AP2 monoclonal antibody even in the presence of mitomycin C-treated T cell-depleted P2 spleen cells as auxiliary cells. In contrast, the B151-TRF2 responses of P1 B cells isolated from both (P1 + P2)----(P1 x P2)F1 and (P1 + P2)----P1 double bone marrow chimeras became sensitive to the inhibition of not only anti-I-AP1 but also anti-I-AP2 monoclonal antibody only when the culture was conducted in the presence of P2 auxiliary cells, demonstrating that they adaptively differentiate to recognize as self-structures allogeneic as well as syngeneic Ia molecules. Moreover, the experiments utilizing B cells from H-2-congenic mice and B cell hybridoma clones as auxiliary cells revealed that B151-TRF2-responsive B cells recognize Ia molecules expressed on B cells. Taken together, these results demonstrate that B151-TRF2-responsive B cells recognize Ia molecules expressed by B cells as self-structures and that their self-recognition specificity is dictated by the MHC haplotype of bone marrow cells present during the B cell ontogeny but not by the MHC haplotype of a radiation-resistant host environment.

Animals↗

PubMed2003

Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration.

Mutations arise in a single individual and at a single point in time and space. The geographic distribution of mutations reflects both historical population size and frequency of migration. We employ coalescence-based methods to coestimate effective population size, frequency of migration, and level of recombination compatible with observed genealogical relationships in sequence data from nine nuclear genes in wild barley (Hordeum vulgare ssp. spontaneum), a highly self-fertilizing grass species. In self-fertilizing plants, gamete dispersal is severely limited; dissemination occurs primarily through seed dispersal. Also, heterozygosity is greatly reduced, which renders recombination less effective at randomizing genetic variation and causes larger portions of the genome to trace a similar history. Despite these predicted effects of this mating system, the majority of loci show evidence of recombination. Levels of nucleotide variation and the patterns of geographic distribution of mutations in wild barley are highly heterogeneous across loci. Two of the nine sampled loci maintain highly diverged, geographic region-specific suites of mutations. Two additional loci include region-specific haplotypes with a much shallower coalescence. Despite inbreeding, sessile growth habit, and the observation of geographic structure at almost half of sampled loci, parametric estimates of migration suggest that seed dispersal is sufficient for migration across the approximately 3,500-km range of the species. Recurrent migration is also evident based on the geographic distribution of mutational variation at some loci. At one locus a single haplotype has spread rapidly enough to occur, unmodified by mutation, across the range of the species.

Biological Evolution↗

PubMed2002

Mitochondrial DNA variation in Pleistocene and modern Atlantic salmon from the Iberian glacial refugium.

Current understanding of the postglacial colonization of Nearctic and Palearctic species relies heavily on inferences drawn from the phylogeographic analysis of contemporary generic variants. Modern postglacial populations are supposed to be representative of their Pleistocene ancestors, and their current distribution is assumed to reflect the different colonization success and dispersal patterns of refugial lineages. Yet, testing of phylogeographic models against ancestral genomes from glacial refugia has rarely been possible. Here we compare ND1 mitochondrial DNA variation in late Pleistocene (16,000-40,000 years before present), historical and contemporary Atlantic salmon (Salmo salar) populations from northern Spain and other regions of western Europe. Our study demonstrates the presence of Atlantic salmon in the Iberian glacial refugium during the last 40,000 years and points to the Iberian Peninsula as the likely source of the most common haplotype within the Atlantic lineage in Europe. However, our findings also suggest that there may have been significant changes in the genetic structure of the Iberian refugial stock since the last ice age, and question whether modern populations in refugial areas are representative of ice age populations. A common haplotype that persisted in the Iberian Peninsula during the Pleistocene last glacial maximum is now extremely rare or absent from European rivers, highlighting the need for caution when making phylogeographic inferences about the origin and distribution of modern genetic types.

Animals↗

PubMed2005

Disturbed population genetics: suspected introgressive hybridization between two Mnais damselfly species (Odonata).

Mnais costalis and M. pruinosa are damselflies (Odonata: Calopterygidae) with low dispersal abilities, both during their aquatic stream-living immature stage and their flying adult stage. A previous nuclear DNA (nDNA) sequencing and morphology study showed that these two species are very closely related, and cohabit widely in western Japan. The two species, however, segregate microhabitats along a stream: M. costalis lives in the lower reaches, and M. pruinosa in the upper reaches. In this study, our analyses were based on mitochondrial DNA (mtDNA), which usually mutates faster and is more variable among individuals than nDNA, and which is inherited maternally. We found that most COI haplotypes were shared between the two species, and that for most study sites interspecific riverine genetic structures were not clarified by mtDNA analysis. Incongruent population genetic structures based on nDNA and mtDNA suggested hybridization and introgression of mtDNA between the two species.

Animals↗

PubMed2006

Comparative analysis of the S-intergenic region in class-II S haplotypes of self-incompatible Brassica rapa (syn. campestris).

In the Brassica self-incompatibility (SI) system, a pollen determinant, SP11, is involved in dominance/recessive relationships in pollen SI phenotypes. In order to gain some insights into the genomic structure around the SP11 and the mechanisms that give dominance/recessive relationships, we characterized the genomic region containing SP11 and SRK genes in three pollen recessive class-II S haplotypes. The direction of transcription of S genes was completely conserved among class-II S haplotypes. However, the region between SP11 and SRK (S-intergenic region) was highly polymorphic without short repetitive sequences. In addition, we found a sequence similarity between the short repetitive sequence and 5'-upstream region of SP11. This sequence similarity was found to be potentially related to the expression of dominance relationships through the change of chromatin structure.

Base Sequence↗

PubMed1995

Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity.

We present an analysis that synthesizes information on the sequence, structure, and motifs of antigenic peptides, which previously appeared to be in conflict. Fourier analysis of T-cell antigenic peptides indicates a periodic variation in amino acid polarities of 3-3.6 residues per period, suggesting an amphipathic alpha-helical structure. However, the diffraction patterns of major histocompatibility complex (MHC) molecules indicate that their ligands are in an extended non-alpha-helical conformation. We present two mutually consistent structural explanations for the source of the alpha-helical periodicity, based on an observation that the side chains of MHC-bound peptides generally partition with hydrophobic (hydrophilic) side chains pointing into (out of) the cleft. First, an analysis of haplotype-dependent peptide motifs indicates that the locations of their defining residues tend to force a period 3-4 variation in hydrophobicity along the peptide sequence, in a manner consistent with the spacing of pockets in the MHC. Second, recent crystallographic determination of the structure of a peptide bound to a class II MHC molecule reveals an extended but regularly twisted peptide with a rotation angle of about 130 degrees. We show that similar structures with rotation angles of 100-130 degrees are energetically acceptable and also span the length of the MHC cleft. These results provide a sound physical chemical and structural basis for the existence of a haplotype-independent antigenic motif which can be particularly important in limiting the search time for antigenic peptides.

Antigens↗

PubMed2004

Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flow?

New Zealand's (NZ) geographical isolation, extensive coastline and well-characterized oceanography offer a valuable system for marine biogeographical research. Here we use mtDNA control region sequences in the abundant endemic sea-star Patiriella regularis to test the following literature-based predictions: that coastal upwelling disrupts north-south gene flow and promotes population differentiation (hypothesis 1); and that an invasive Tasmanian population of the species was introduced anthropogenically from southern New Zealand (hypothesis 2). We sequenced 114 samples from 22 geographical locations, including nine sites from North Island, nine from South Island, one from Stewart Island and three from Tasmania. Our analysis of these sequences revealed an abundance of shallow phylogenetic lineages within P. regularis (68 haplotypes, mean divergence 0.9%). We detected significant genetic heterogeneity between pooled samples from northern vs. southern New Zealand (FST = 0.072; P = 0.0002), consistent with the hypothesis that upwelling disrupts gene flow between these regions (hypothesis 1). However, we are currently unable to rule out the alternative hypothesis that Cook Strait represents a barrier to dispersal (North Island vs. South Island; FST = 0.031; P = 0.0467). The detection of significant spatial structure in NZ samples is consistent with restricted gene flow, and the strong structure evident in northern NZ may be facilitated by distinct ocean current systems. Four shared haplotypes and nonsignificant differentiation (FST = 0.025; P = 0.2525) between southern New Zealand and Tasmanian samples is consistent with an anthropogenic origin for the latter population (hypothesis 2).

Animals↗

PubMed1985

Thymus-leukemia (TL) antigens of the mouse. Analysis of TL mRNA and TL cDNA TL+ and TL- strains.

A thymus-leukemia (TL)-specific probe, pTL1, has been generated from a TL-coding gene of BALB/c mice. Multiple species of TL mRNA were detected in TL+ cells by Northern blot analysis with pTL1, and different Tla haplotypes could be distinguished on the basis of characteristic patterns of TL mRNA. No TL-related message was found in normal or leukemic TL- cells, including thymocytes from Tlab mice. However, TL mRNA could be detected in TL+ leukemias occurring in Tlab mice. A cDNA library has been made from ASL1 (a TL+ leukemia of A mice [Tlaa]), and pTL1+ clones have been sequenced. At least three structurally distinct TL genes are expressed in ASL1. Sequence comparison of TL genes from three Tla haplotypes indicates that TL genes are highly conserved (greater than 90% homology) and are more distantly related to H-2 genes. Several polyadenylation sites have been found in the 3' untranslated region of TL genes, and differential polyadenylation contributes to the size heterogeneity of TL transcripts. The predicted amino acid sequence of TL products indicates that TL and H-2 are similar in domain structure and disulfide bonds, but differ in glycosylation sites and in cytoplasmic domain sequences.

Amino Acid Sequence↗

PubMed2002

Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize.

The 140-kb a1-sh2 interval of the maize genome contains at least four genes (a1, yz1, x1, and sh2). Partial sequence analysis of two haplotypes has revealed many single nucleotide polymorphisms and InDel polymorphisms, including several large structural polymorphisms. The physical positions of 101 meiotic recombination breakpoints are not distributed uniformly across the interval and are instead concentrated within three recombination hot spots. Two of these recombination hot spots are genic (a1 and yz1) and one is apparently nongenic. The x1 gene is not a recombination hot spot. Thus, these results suggest that not all hot spots are genes and indicate that not all genes are hot spots. Two of the 101 recombination events arose by means of either noncrossover events involving conversion tract lengths of at least 17 kb or double-crossover events. Only one recombination breakpoint mapped to the approximately 80-kb distal portion of the a1-sh2 interval that contains large amounts of repetitive DNA including retrotransposons; in this region the ratio of genetic to physical distance is less than 0.5% of the genome's average. These results establish that the retrotransposon faction of the maize genome is relatively inert recombinationally.

Alleles↗