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Results for “Haplotype structures”

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PubMed2005

Variation in DISC1 affects hippocampal structure and function and increases risk for schizophrenia.

Disrupted-in-schizophrenia 1 (DISC1) is a promising schizophrenia candidate gene expressed predominantly within the hippocampus. We typed 12 single-nucleotide polymorphisms (SNPs) that covered the DISC1 gene. A three-SNP haplotype [hCV219779 (C)-rs821597 (G)-rs821616 (A)] spanning 83 kb of the gene was associated with schizophrenia in a family-based sample (P = 0.002). A common nonconservative SNP (Ser704Cys) (rs821616) within this haplotype was associated with schizophrenia (P = 0.004). Based on primary expression of DISC1 in hippocampus, we hypothesized that allelic variation at Ser704Cys would have a measurable impact on hippocampal structure and function as assayed via specific hippocampus-related intermediate phenotypes. In addition to overtransmission in schizophrenia, the Ser allele was associated with altered hippocampal structure and function in healthy subjects, including reduced hippocampal gray matter volume and altered engagement of the hippocampus during several cognitive tasks assayed with functional magnetic resonance imaging. These convergent data suggest that allelic variation within DISC1, either at Ser704Cys or haplotypes monitored by it, increases the risk for schizophrenia and that the mechanism of this effect involves structural and functional alterations in the hippocampal formation.

Adult↗

PubMed2005

Genetics of individual differences in bitter taste perception: lessons from the PTC gene.

The ability or inability to taste the compound phenylthiocarbamide (PTC) is a classic inherited trait in humans and has been the subject of genetic and anthropological studies for over 70 years. This trait has also been shown to correlate with a number of dietary preferences and thus may have important implications for human health. The recent identification of the gene that underlies this phenotype has produced several surprising findings. This gene is a member of the T2R family of bitter taste receptor genes. It exists in seven different allelic forms, although only two of these, designated the major taster and major non-taster forms, exist at high frequency outside sub-Saharan Africa. The non-taster allele resides on a small chromosomal region identical by descent, indicating that non-tasters are descended from an ancient founder individual, and consistent with an origin of the non-taster allele preceding the emergence of modern humans out of Africa. The two major forms differ from each other at three amino acid positions, and both alleles have been maintained at high frequency by balancing natural selection, suggesting that the non-taster allele serves some function. We hypothesize that this function is to serve as a receptor for another, as yet unidentified toxic bitter substance. At least some of the remaining five haplotypes appear to confer intermediate sensitivity to PTC, suggesting future detailed studies of the relationships between receptor structure and taste function.

Alleles↗

PubMed1988

A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations.

Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candidate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.

Alcohol Dehydrogenase↗

PubMed2005

Extensive polymorphisms of LILRB1 (ILT2, LIR1) and their association with HLA-DRB1 shared epitope negative rheumatoid arthritis.

Leukocyte immunoglobulin-like receptor subfamily B member 1 (LILRB1/LIR1/ILT2) is an inhibitory receptor broadly expressed on leukocytes and recognizes HLA-class I and human cytomegalovirus UL18. LILRB1 is encoded within the leukocyte receptor complex on 19q13.4, previously implicated to be a susceptibility region to systemic lupus erythematosus (SLE). In this study, we screened for polymorphisms of LILRB1 and examined their association with SLE and rheumatoid arthritis (RA). In the 5' portion of LILRB1, three haplotypes containing four non-synonymous substitutions within the ligand-binding domains and two single nucleotide polymorphisms within the promoter region were identified and designated as PE01-03. In the 3' portion, two haplotypes (CY01, 02) containing a non-synonymous substitution of the cytoplasmic region were identified. CY01 and 02 did not co-segregate with PE01-03. Significant association with susceptibility to SLE or RA was not observed; however, among the subjects not carrying RA-associated HLA-DRB1 shared epitope (SE), LILRB1.PE01/01 diplotype was significantly associated with RA (odds ratio 2.05, P = 0.019 and Pc = 0.038). Gross difference was not observed in the crystal structures, thermostabilities and binding affinities to HLA-class I ligands among LILRB1.PE01-03 haplotype products; however, surface expression of LILRB1 was significantly decreased in lymphocytes and monocytes from the carriers of PE01 haplotype. These findings demonstrated that LILRB1 is highly polymorphic and is associated with susceptibility to RA in HLA-DRB1 SE negative subjects, possibly by insufficient inhibitory signaling in leukocytes. In addition, these observations suggested that the polymorphisms of LILR family members may be substantially involved in the diversity of human immune responses.

Adult↗

PubMed1994

Defining the Rh blood group antigens. Biochemistry and molecular genetics.

The Rh blood group antigens (D, Cc and Ee series) are carried by a family of non glycosylated hydrophobic transmembrane proteins of 30-32 kDa which are missing from the red cells of rare Rhnull individuals that express several membrane defects. The structure of these proteins has been deduced from cDNA cloning and studies have shown that the Rh proteins are erythroid specific and share no sequence homology with any known protein. The RhD and non-D proteins exhibit 92% sequence identity and their predicted membrane topology is similar as most of the molecules appear to reside between the leaflets of the phospholipid bilayer with only short hydrophilic loops connecting the twelve putative transmembrane helices. The RHD and RHCE genes encoding the Rh proteins (D and Cc/Ee, respectively) are organized in tandem on chromosome 1p34-p36 and most likely derived by duplication of a common ancestral gene. This concept is supported by the identification of RH-like genes in non human primates. The human RH locus is best described as a two-gene model in which all RhD-positive and most RhD-negative haplotypes are composed of two (RHD and RHCE) or only one (RHCE) structural genes, respectively. The RHD gene encodes the D protein and the RHCE gene encodes the C/c and E/e proteins presumably by alternative splicing of a pre messenger RNA. The correlation between the blood group D epitopes and the amino acid polymorphism of the Rh proteins is not yet established, but amino acid polymorphisms at positions 103 and 226 determine the molecular basis for the C/c (Ser-->Pro) and E/e (Pro-->Ala) specificities, respectively. Most variants analyzed so far are caused by gene conversion which appears as the principal mechanism responsible for polymorphism and gene diversity in the RH system. However, gene deletions have also been found in some occasions. To date, all Rhnull phenotypes investigated most likely result from transcriptional regulatory mechanisms that are not yet understood. Rhnull individuals suffer a clinical syndrome of varying severity and their red cells are characterized by morphological and functional abnormalities of cation transport and phospholipid asymmetry. In addition, several membrane components including the Rh proteins and other glycoproteins recently characterized (Rh50 glycoprotein, CD47, glycophorin B, Duffy, LW) are absent or severely decreased on these cells. These findings suggest that the Rh proteins are assembled into a multimeric complex with these glycoproteins and further studies should clarify the role in biosynthesis and the potential function of each component in this complex.

Amino Acid Sequence↗

PubMed2000

The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies.

The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR-RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale.

Chenopodiaceae↗

PubMed2007

Pleistocene isolation and recent gene flow in Haliotis asinina, an Indo-Pacific vetigastropod with limited dispersal capacity.

Haliotis asinina is a broadcast-spawning mollusc that inhabits Indo-Pacific coral reefs. This tropical abalone develops through a nonfeeding larval stage that is competent to settle on specific species of coralline algae after 3-4 days in the plankton. Failure to contact an inductive algae within 10 days of hatching usually results in death. These life cycle characteristics suggest a limited capacity for dispersal and thus gene flow. This makes H. asinina particularly suitable for elucidating phylogeographical structure throughout the Indo-Malay Archipelagoes, and eastern Indian and western Pacific Oceans, all regions of biogeographical complexity and high conservation value. We assayed 482 bp of the mitochondrial cytochrome oxidase II gene in 206 abalone collected from 16 geographically discrete sites across the Indian and Pacific Oceans and Indo-Malay Archipelagoes. DNA sequence variation was analysed via population genetics and phylogenetics, and by nested clade analyses (NCA). Our data resolved clear phylogeographical breaks among major biogeographical regions, with sequence divergences ranging from a high of 3.7% and 3.0% between Indian and Pacific sites and Pacific and Indo-Malay sites, respectively, to a low of 1.1% between Indian and Indo-Malay sites. Despite the apparent limited dispersal capacity of H. asinina, no finer scale phylogeographical structure was resolved within the respective biogeographical regions. However, amova and NCA identified several significant associations between haplotypes and geographical distribution, most notably higher gene flow among geographical populations associated with major ocean currents. Our study provides further evidence that larval dispersal capacity alone is not a good predictor of population genetic structure in marine invertebrates. We infer instead that a combination of historical events (long-term barriers followed by range expansion associated with Pleistocene sea level changes) and contemporary processes (gene flow restricted by life history and oceanography) have shaped observed patterns of H. asinina phylogeography.

Animals↗

PubMed1987

Establishment of embryonic stem cell lines from preimplantation mouse embryos homozygous for lethal mutations in the t-complex.

We have determined the frequency at which embryonic stem cell (ESC) lines can be established from inner cell masses (ICMs) isolated from blastocysts homozygous for lethal mutations in the mouse t-complex. Approximately one-third of the expected number, 3/29, of the ESC lines established from embryos obtained by inter-se mating of +/tw18 mice are homozygous for the tw18 haplotype. These tw18/tw18 ESC lines form a variety of cell types in vitro and in vivo, including mesodermal derivatives such as cartilage and muscle. On the basis of these and data from other studies, we suggest that the normal function of the gene represented by the tw18 lethal allele is required for multiplication/survival of mesodermal precursors in the embryo rather than the specification of the mesodermal lineage, and that the lethal effects of this mutation are expressed in only the highly structured environment of the early postimplantation embryo. In studies of the lethal tw5 haplotype, we found that 2/2 ESC lines obtained are mutant homozygotes. Analysis of these data, in conjunction with the results of our earlier study (Magnuson, T., Epstein, C. J., Silver, L. M., and Martin, G. R. (1982), Nature (London) 298, 750-753), suggests that homozygosity for the genes found in the tw5 haplotype does not reduce cell viability. By contrast, 0/16 ESC lines isolated from embryos obtained from matings of +/t0 mice are mutant homozygotes. Analysis of the genotypes of ICM-derived primary stem cell colonies suggests that t0 homozygous ICM cells are unable to undergo sufficient proliferation in vitro to give rise to ESC lines.

Animals↗

PubMed2001

Population structure and biogeography of migratory freshwater fishes (Prochilodus: Characiformes) in major South American rivers.

Mitochondrial DNA (mtDNA) sequences were used to infer the phylogenetic relationships of Prochilodus species in the Paraná, Amazonas, Orinoco, and Magdalena basins. Sequences of ATPase subunits 6 and 8 (total 840 bp) were obtained for 21 Prochilodus specimens from the four river systems. Using Semaprochilodus as an outgroup, phylogenetic analyses showed that: (i) each river basin contains a monophyletic group of mtDNA lineages; and (ii) the branching order places Magdalena in a basal position with subsequent branching of Orinoco, Amazon and Paraná. The mitochondrial control region was sequenced for 26 P. lineatus (from the Paraná basin) and six other Prochilodus specimens from the Magdalena, Orinoco and Amazon. All 26 control region haplotypes were unique with sequence divergence ranging from 0.3 to 3.6%. The control region phylogeny is well resolved but phylogenetic structure is not associated with geography. For example, mtDNA haplotypes from the upper Paraná (Mogui Guassú) and the upper Bermejo, separated by at least 2600 km, have close genealogical ties. Phylogeographic analyses, including nested clade analysis, suggest high levels of gene flow within this basin.

Animals↗

PubMed2004

[Principal component analysis of Y-chromosome haplotype distribution in 18 ethnic groups in Yunnan Province].

Based on the historical records, 18 of the 26 ethnic groups in Yunnan Province are the descendant populations of three ancient tribes, Bai-Yue, Bai-Pu and Di-Qiang, linguistically belonging to the Daic, Austro-Asiatic and Tibeto-Burman, respectively. In order to trace the origins of these native ethnic groups, a total of 13 East Asian specific Y-chromosome biallelic markers were used to study the genetic structure of 20 local populations covering all the 18 ethnic groups in Yunnan Province. Haplotypes were analysis by PCR-RFLP method. Our results showed that H11 and H12 were the predominant haplotypes in the descendant populations of Bai-Yue tribe. H5, H6 and H8 were the dominant haplotypes in Di-Qiang descendants, and the frequencies of H6, H8 and H11 were very high in the descendant populations of Bai-Pu. To investigate relationships among 20 populations, a three dimensional PC analysis were performed based on the distribution of the 13 haplotypes. All populations were divided into two clusters in the PC plot. The first cluster was mainly composed by the descendant populations of Bai-Yue, and the second one was mainly composed by the descendants of Di-Qiang tribe. This result indicated that Bai-Yue and Di-Qiang's paternal lineage had different origins, which was in agreement with the historical documents and linguistic classification.

Asian People↗

PubMed2003

Some notes on the combinatorial properties of haplotype tagging.

Tagging haplotypes with a small number of genetic markers is becoming an increasingly interesting and important problem. Surprisingly little work has been done to characterize the mathematical framework of this problem. In this paper we present a mathematical frame, based on Boolean algebras, that adequately describe the structure of a set of genetic bi-allelic markers and the corresponding set of haplotypes. We derive a number of results that relate the number of markers required to tag a set of haplotypes to the set of markers themselves.

Alleles↗

PubMed2004

Phylogeography of the Patelloida profunda group (Gastropoda: Lottidae): diversification in a dispersal-driven marine system.

In the last decade, greater than expected levels of genetic structure have been reported for many marine taxa with high dispersal capabilities. Although little-studied to date, it is predicted that taxa with poor dispersal abilities would exhibit even more genetic differentiation than high dispersal taxa. These systems may track biogeographical processes better than more dispersive taxa and, more critically, function as the 'lowest common denominators' in MPA design initiatives. We investigate phylogeographical patterns in the poorly dispersing, yet widely distributed Patelloida profunda group and related congeners across the Indo-west Pacific region. One hundred and twenty-five individuals were sequenced for COI mtDNA [593 base pairs (bp)] and 44 individuals were sequenced for 16S mtDNA (539 bp). Identified P. profunda group lineages are highly geographically structured, with 12 reciprocally monophyletic lineages reported from 13 localities. Divergences within Indian and Pacific basins range from d = 0.013 to 0.127 and between basins from d = 0.147 to 0.197. The latter split is ancient (> 15 Myr) and cannot be related to Plio-Pleistocene sea-level fluctuations, characteristic of previously reported divergences in the same region. Juxtaposed against this structure is genetic connectivity between two widely separated P. profunda populations that share a common haplotype (phiST = 0.001). This finding contrasts with previous work in the same geographical region and cautions strongly against single taxon indicators for designing conservation priorities or marine protected areas (MPAs). Historical and/or biological factors may play more significant roles than oceanography alone in determining the genetic structuring of taxa. In light of these findings, we discuss the difficulty in deriving biogeographical process or directionality from phylogenetic trees in dispersal-driven systems. Even with a well-resolved, highly supported topology, many equally parsimonious scenarios are possible.

Animals↗

PubMed1995

Polymorphism in the beta chain of IAq versus IAp influences presentation of protein but not peptide antigens.

T cells play a critical role in the development of collagen-induced arthritis (CIA). Immunization with heterologous (chick) type II collagen (cII) results in chronic inflammation with progressive damage to the joints. The expression of specific MHC Class II alpha beta dimers, including IAq, is critical to induction of disease. The alpha chains of IAq and IAp are identical in sequence. The IAq and IAp beta chains differ by only four amino acid residues: 85, 86, 88, and 89. However, mice of the H-2p haplotype are not susceptible to CIA. To examine the impact of these structural differences in IA molecules on T cell Ag recognition, we studied presentation of cII peptides and denatured cII by APCs obtained from H-2q and H-2p mice. We also assessed presentation of ovalbumin, myelin basic protein (MBP), and MBP peptides by these APC populations. H-2q APCs presented both peptides and proteins to our T cell hybrids. In contrast, APCs obtained from H-2p mice presented peptides, but were defective in the processing and/or presentation of protein Ags. We then altered pairs of the residues in IAq to those found in IAp using site-directed mutagenesis and transfected these constructs into M 12.C3 B cells. All transfectants were able to present peptides, but those expressing IAp were unable to present protein Ags. The use of transfectants expressing hybrid molecules (residues 85 and 86 from IAp, 88 and 89 from IAq, or vice versa) allowed us to localize the region responsible for this defect to residues 85 and 86 of the beta chain. The presence of IAp residues (glu and thr versus gly and val in IAq) at these sites severely compromised the capacity for protein presentation. Resistance to CIA in H-2p haplotype mice may be a reflection of the limited repertoire of epitopes to which these mice can respond relative to susceptible H-2q mice.

Amino Acid Sequence↗

PubMed2000

Genetic diversity and gene flow among southeastern Queensland koalas (Phascolarctos cinereus).

Habitat fragmentation and destruction associated with the rapid urban and rural development of southeast Queensland presents an immediate threat to the survival of koala populations within this region. A sensitive method combining heteroduplex analysis (HDA) with temperature gradient gel electrophoresis (TGGE) was optimized to detect within-species variation in a mitochondrial DNA (mtDNA) control-region fragment, approximately 670 bp in length, from the koala. Eight different haplotypes were characterized in koalas, of which four were novel. Analysis of mtDNA diversity in 96 koalas from five populations in southeast Queensland revealed that the number of haplotypes in a single population ranged from one to five, with an average within-population haplotype diversity of 0.379 +/- 0.016, and nucleotide diversity of 0.22 +/- 0.001%. Nucleotide divergence between populations averaged 0.09 +/- 0.001% and ranged from 0.00 to 0.14%. Significant genetic heterogeneity was observed among most populations, suggesting that koala populations may be spatially structured along matrilines, although this may not be universal. The limited distribution of the central phylogenetic haplotype suggested the possibility of historical population bottlenecks north of the Gold Coast, while the presence of two highly divergent haplotypes at the Moreton site may indicate the occurrence of one or more undocumented translocation events into this area.

Animals↗

PubMed1994

Physical and genetic mapping of the serpin gene cluster at 14q32.1: allelic association and a unique haplotype associated with alpha 1-antitrypsin deficiency.

The alpha 1-antitrypsin (PI) gene is part of a cluster of structurally related serine protease inhibitor genes localized at chromosome 14q32.1, a cluster that includes the alpha 1-antichymotrypsin (AACT), protein C inhibitor (PCI), and corticosteroid-binding globulin (CBG) genes and the alpha 1-antitrypsin-like pseudogene (PIL). The order of the genes is refined here by genetic mapping using simple tandem repeat polymorphisms (STRPs) and by physical mapping in YACs. The order of the genes is (centromere)-CBG-PIL-PI-PCI-AACT-(telomere). Analysis of DNA haplotypes comprising STRP and RFLP markers in the serpin genes reveals considerable allelic association throughout the cluster. Furthermore, the common alpha 1-antitrypsin deficiency allele, PI*Z, has a unique DNA haplotype at the CBG, PIL, and PI loci, which extends over 60 kb in 97% of cases and in 44% of cases includes the PCI and AACT loci. This unique haplotype will be of use in examining a number of other diseases, particularly those with an inflammatory component, thought to be associated with alpha 1-antitrypsin deficiency or partial deficiency.

Alleles↗

PubMed2002

DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis).

Uniparentally inherited mitochondrial (mt)DNA and chloroplast (cp)DNA microsatellites (cpSSRs) were used to examine population genetic structure and biogeographic patterns of bird-dispersed seed and wind-disseminated pollen of whitebark pine (Pinus albicaulis Engelm.). Sampling was conducted from 41 populations throughout the range of the species. Analyses provide evidence for an ancestral haplotype and two derived mtDNA haplotypes with distinct regional distributions. An abrupt contact zone between mtDNA haplotypes in the Cascade Range suggests postglacial biogeographic movements. Among three cpSSR loci, 42 haplotypes were detected within 28 cpSSR sample populations that were aggregated into six regions. Analysis of molecular variance (amova) was used to determine the hierarchical genetic structure of cpSSRs. amova and population pairwise comparisons (FST ) of cpSSR, and geographical distribution of mtDNA haplotypes provide insights into historical changes in biogeography. The genetic data suggest that whitebark pine has been intimately tied to climatic change and associated glaciation, which has led to range movements facilitated by seed dispersal by Clark's nutcracker (Nucifraga columbiana Wilson). The two hypotheses proposed to explain the genetic structure are: (i) a northward expansion into Canada and the northern Cascades in the early Holocene; and (ii) historical gene flow between Idaho and the Oregon Cascades when more continuous habitat existed in Central Oregon during the late Pleistocene. Genetic structure and insights gained from historical seed movements provide a basis on which to develop recovery plans for a species that is at risk from multiple threats.

Animals↗

PubMed1991

Molecular structure of Tcp-10 genes from the t complex responder locus.

Male transmission ratio distortion (TRD) is a property of mouse t haplotypes which requires the t complex responder locus (Tcr). Tcr has been localized to a 70-160 kb region in t haplotypes. A candidate gene for the responder, called Tcp-10bt, has been cloned and is one member of a highly related gene family called Tcp-10 (formerly T66). Molecular evidence suggests that unique alternative splicing of the Tcp-10bt gene may be responsible for the mutant responder activity. Here we present the intron/exon structure of a representative Tcp-10 gene, and the characterization of alternative polyadenylation sites. The Tcp-10 genes contain 12 exons which span approximately 21 kb of DNA. At least six different polyadenylation sites are used, and none have a perfect consensus signal. This appears to be a common feature associated with testes-expressed transcripts. Since the gene we have analyzed is absent from many t haplotypes without apparent consequence, and no corresponding cDNAs have been isolated, it was speculated to be a pseudogene. However, no major sequence differences were found within the coding sequence to conclude that Tcp-10pst is a pseudogene.

Amino Acid Sequence↗

PubMed2005

Selection on the structural stability of a ribosomal RNA expansion segment in Daphnia obtusa.

The high rate of sequence divergence in nuclear ribosomal RNA (rRNA) expansion segments offers a unique opportunity to study the importance of natural selection in their evolution. To this end, we polymerase chain reaction amplified and cloned a 589-nt fragment of the 18S rRNA gene containing expansion segments 43/e1 and 43/e4 from six individual Daphnia obtusa from four populations. We screened 2,588 clones using single-stranded conformation polymorphism analysis and identified 103 unique haplotype sequences. We detected two pairs of indel sites in segment 43/e4 that complement each other when the secondary structure of the linear sequence is formed. Seven of the 12 observed combinations of length variants at these four sites (haplotypes) are shared between individuals from different populations, which may suggest that some of the length variation was present in their common ancestor. Haplotypes with uncompensated indels were only observed at low frequencies, while compensated indel haplotypes were found at a wide range of frequencies, supporting the hypothesis that the energetic stability of expansion segments is a trait under natural selection. In addition, there was strong linkage disequilibrium between the four complementary indel sites, particularly those that pair with one another in the secondary structure. Despite selection against unpaired bulges at these four indel sites, some nucleotides that form unpaired bulges are highly conserved in segment 43/e4, indicating that they are under a different selective constraint, possibly due to their role in higher level structural interactions.

Animals↗