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PubMed2000

Archaic lineages in the history of modern humans.

An important question in the ongoing debate on the origin of Homo sapiens is whether modern human populations issued from a single lineage or whether several, independently evolving lineages contributed to their genetic makeup. We analyzed haplotypes composed of 35 polymorphisms from a segment of the dystrophin gene. We find that the bulk of a worldwide sample of 868 chromosomes represents haplotypes shared by different continental groups. The remaining chromosomes carry haplotypes specific for the continents or for local populations. The haplotypes specific for non-Africans can be derived from the most frequent ones through simple recombination or a mutation. In contrast, chromosomes specific for sub-Saharan Africans represent a distinct group, as shown by principal component analysis, maximum likelihood tree, structural comparison, and summary statistics. We propose that African chromosomes descend from at least two lineages that have been evolving separately for a period of time. One of them underwent range expansion colonizing different continents, including Africa, where it mixed with another, local lineage represented today by a large fraction of African-specific haplotypes. Genetic admixture involving archaic lineages appears therefore to have occurred within Africa rather than outside this continent, explaining greater diversity of sub-Saharan populations observed in a variety of genetic systems.

Africa↗

PubMed2006

Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis).

Climatic oscillations during the Pleistocene ice ages produced great changes in species' geographical distribution and abundance, which could be expected to have genetic consequences. Living in the temperate upwelling zones of the northwestern Pacific, Japanese anchovy (Engraulis japonicus) might have been affected by these severe climatic oscillations. To investigate the effects of Pleistocene climatic changes on the evolution in Japanese anchovy, fragments of 522 bp at the 5' end of mitochondrial DNA control region were sequenced for 241 individuals from 13 localities and 37 individuals of Australian anchovy. Japanese anchovy and Australian anchovy are reciprocally monophyletic and a late Pleistocene transequatorial divergence between the two species was indicated. High levels of haplotype diversity (>0.99) were found for all samples, indicating a high level of genetic diversity. Analyses of molecular variance and the conventional population statistic F(ST) revealed no significant genetic structure throughout the range of Japanese anchovy. Both mismatch distribution analyses and neutrality tests suggested a late Pleistocene population expansion for both Japanese anchovy (79,000-317,000 years ago) and Australian anchovy (45,000-178,000 years ago).

Animals↗

PubMed2002

Computer-based design of an HLA-haplotype and HIV-clade independent cytotoxic T-lymphocyte assay for monitoring HIV-specific immunity.

BACKGROUND: Human immunodeficiency virus (HIV)- specific CD8-positive cytotoxic T-lymphocytes (CTL) play a key role in controlling HIV infection. Monitoring CTL response could be clinically relevant during structured therapy interruption (STI), HIV exposure, and vaccine trials. However, HLA patients' restriction and HIV variability limited the development of a CTL assay with broad specificity. MATERIALS AND METHODS: We designed an HLA-class I/HIV-1 clade independent assay for assessing HIV- specific CTL by using a computer-assisted selection ofthe CTL epitopes. Twenty-eight 15-mers were selected by peptide-binding motifs analysis using different databases (HIV-Immunology Database, SYFPEITHI, BIMAS). Altogether they putatively bind to more than 90% of HLA haplotypes in different populations, with an overall HIV-1 variability below 9%. The peptide pool was used as an antigen in an intracellular cytokine staining (ICS) assay for quantifying HIV-specific CTL response. RESULTS: The test can be performed using both fresh and cryopreserved peripheral blood mononuclear cells (PBMC), whereas GAG protein as antigen works only on fresh PBMC. A significantly higher CTL response with respect to HIV-negative controls was detected in all HIV-1 infected subjects of two groups of patients with different ethnicities (Caucasians and Africans) and coming from areas with different HIV-1 clade prevalences (clade B and A/G, respectively). In Caucasian patients, after month of STI, the number of HIV-1 specific CTL (2,896 +/- 2,780 IFN-gamma specific CD8 cells/ml) was significantly higher than that found at enrolment (2,125 +/- 4,426 IFN-gamma specific CD8 cells/ml, p< 0.05). CONCLUSIONS: These data indicate that this CTL assay is broadly specific and could represent a useful clinical tool for HIV immunodiagnostic independent of HLA-haplotype and HIV-clade variabilities.

Adult↗

PubMed2005

Population genetic structure of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis): implications for management and conservation.

Understanding the population genetic structure is a prerequisite for conservation of a species. The degree of genetic variability characteristic of the mitochondrial DNA control region has been widely exploited in studies of population genetic structure and can be useful in identifying meaningful population subdivisions. To estimate the genetic profile of the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), an endangered freshwater population endemic to China, the complete mtDNA control region was examined in 39 individuals belonging to seven different stocks inhabiting the middle and lower reaches of the Yangtze River. Very low genetic diversity was found (nucleotide diversity 0.0011 +/- 0.0002 and haplotypic diversity 0.65 +/- 0.05). The mtDNA genetic pattern of the Yangtze population appears to indicate a founder event in its evolutionary history and to support the marine origin for this population. Analyses by Fst and phi(st) yielded statistically significant population genetic structure (Fst = 0.44, P < 0.05; phi(st) = 0.36, P < 0.05). These results may have significant implications for the management and conservation of the Yangtze finless porpoise in the future.

Animals↗

PubMed2001

Mitochondrial DNA variation in the highly endangered cyprinid fish Anaecypris hispanica: importance for conservation.

Anaecypris hispanica is a cyprinid fish which is endemic to the Guadiana River basin in the Iberian Peninsula, and whose abundance and geographical range have contracted considerably during the last 20 years. We investigated mitochondrial DNA cytochrome b and control region variation among specimens representative of nine tributaries, using direct sequencing and diagnostic restriction fragment length polymorphism. The samples from the Caia, Degebe, Ardila, and Odeleite rivers exhibited haplotypes that differed by a large number of site differences, which may be indicative of population bottlenecks that have caused stochastic extinction of haplotypes. In contrast, the populations from the Xévora, Chança, Carreiras, Vascão and Foupana rivers exhibited low levels of nucleotide diversity, which together with high haplotype diversity may also be indicative of genetic bottleneck events, with subsequent population expansion. Phylogenetic analyses, a minimum spanning network, and an analysis of molecular variance revealed geographical structuring, suggesting limited or no gene flow between populations. The populations from extreme southern rivers (Foupana and Odeleite) are monophyletic entities, suggesting that they have been isolated, probably as a consequence of brackish water upstream of their confluence with the Guadiana. The results suggest that the Foupana and the Odeleite populations, and the remaining northern populations altogether should be managed as three distinct Evolutionary Significant Units (ESUs). Within the northern ESU, four Management Units (MUs) should be considered.

Animals↗

PubMed2001

Sequence comparisons among dispersed members of the Brassica S multigene family in an S9 genome.

Self-incompatibility (SI) systems prevent self-pollination and promote outbreeding. In Brassica, the SI genes SLG (for S-locus glycoprotein) and SRK (for S-receptor kinase) are members of the S multigene family, which share the SLG-like domain (S domain), which encodes a putative receptor. We have cloned members of the S multigene family from the S9 haplotype of B. campestris (syn. rapa). In addition, eight distinct genomic regions harboring 10 SLG/SRK-like genes were characterized in the present study. Sequence analysis revealed two novel SRK-like genes, BcRK3 and BcRK6 (for B. campestris receptor kinases 3 and 6, respectively). Other genes that were characterized included SFR2 (for S gene family receptor 2), SLR2 (for S locus related gene 2), and a pseudogene. Based on phylogenetic analysis of the nucleotide sequences of the S domain regions, SLG and SRK appear to be distinct from other members of the S multigene family. Linkage analysis showed that most members of the S multigene family are dispersed in the Brassica genome, and that SLR1 (S locus related gene 1) is not linked to the SLR2 in B. campestris.

Blotting, Southern↗

PubMed2006

Variations in two gene sequences of Citrus tristeza virus after host passage.

We estimated genetic variation in two groups of Citrus tristeza virus (CTV) isolates: one of them (isolates T385, T317, T318 and T305) derived from a Spanish source by successive host passages, and the other (isolates T388 and T390), obtained after aphid transmission of a Japanese source. The population structure of these isolates had been characterized by single-strand conformation polymorphism analysis of genes p18 and p20. The nucleotide sequences of representative haplotypes of each isolate and gene were used to estimate genetic diversity within and between isolates and to evaluate genetic differentiation between populations. Phylogenetic analysis of p18 and p20 sequence variants showed two main groups: one them included variants predominant in the severe isolates (T318, T305 and T388), and the other comprised variants present in both mild (T385, T317) and severe isolates. Most sequence variants of isolate T390 were not associated to these groups. In some isolates, within-isolate diversity was higher than diversity with other isolates because their population contained distantly related sequence variants, some of which were genetically close to variants predominant in the second isolate. Isolates T388 and T390 were genetically different for the two genes, as estimated by the F statistic. Furthermore, genetic differentiation between T385 and T317, T318 and T305 increased after each host passage. Our results suggest that aphid transmission and host passage may significantly alter the composition of CTV populations and thus be an important factor in their evolution.

Base Sequence↗

PubMed1991

Identification of variable simple sequence motifs in 19q13.2-qter: markers for the myotonic dystrophy locus.

Variable simple sequence motifs (VSSMs), or microsatellites, were used for the genetic delimitation of the myotonic dystrophy (DM) region at 19q. Three simple sequence motifs were identified in and around the ERCC1 DNA-repair gene at 19q13.2-13.3 and one in the vicinity of the RRAS gene at 19q13.3-qter. A (TG)n repeat, situated within the ninth intron of the ERCC1 gene, was converted into a highly informative multiallelic marker using PCR-mediated DNA amplification and high-resolution gel analysis. The structurally similar sequence motif in the RRAS gene yielded a marker system with only two alleles. Use of these VSSMs for linkage analysis and haplotyping in a selected set of DM families revealed that the DM gene is distal but close to the ERCC1 locus and can be excluded from the CKM-ERCC1 interval at 19q13.2. The order for RRAS and other distally located markers was established as DM-D19S50-[RRAS,KLK]-D19S22-ter.

Alleles↗

PubMed2005

Intraspecific variation in fem-3 and tra-2, two rapidly coevolving nematode sex-determining genes.

The sex determination gene fem-3 encodes one of the most divergent proteins yet described in the terrestrial nematode Caenorhabditis. Despite this rapid sequence change, however, FEM-3 is essential for male development in the three species surveyed thus far. It also participates in conserved protein-protein complexes with the transmembrane receptor TRA-2 and the phosphatase FEM-2 in these species. These interactions show strong species specificity, indicating that conserved residues are not sufficient for function and that compensatory evolution between binding partners is important. To shed further light on the nature of this coevolution, and to discern the extent of amino acid polymorphism allowed in FEM-3 and the domain of TRA-2 that binds it, we have examined intraspecific variation in the gonochoristic species Caenorhabditis remanei. Ten new complete Cr-fem-3 alleles from three regions of the United States are described. We also obtained sequences for the FEM-3-binding domain of TRA-2 for 9 of the same strains. These alleles were compared with each other, with the European founder alleles, and with the orthologous sequences from the congeners Caenorhabditis elegans and C. briggsae. We find that FEM-3 harbors abundant amino acid polymorphisms along its entire length. The majority (but not all) of these occur in nonconserved residues, and in at least one domain there is evidence for diversifying selection. The FEM-3-binding domain of TRA-2 is less polymorphic than FEM-3. Amino acids neither polymorphic nor conserved between species are candidates for residues mediating species-specific interaction of FEM-3 with its binding partners.

Alleles↗

PubMed2006

The argRB of Escherichia coli is rare in isolates obtained from natural sources.

A single nucleotide polymorphism between Escherichia coli strains K12 and B is known to alter the mechanism by which the arginine repressor regulates arginine biosynthesis, from a regulated system in E. coli K12 to a deregulated system in E. coli B. Laboratory experiments have demonstrated that the different regulatory strategies are selectively favored under different environmental conditions. In this study we analyzed 537 E. coli strains and show that the argR allele in E. coli B, which causes deregulation, is rare in isolates obtained from natural sources. Moreover, sequence analysis of 85 strains shows no evidence of selection at the arginine repressor locus. This illustrates that analysis of sequence data is insufficient to detect selection of uncommon alleles in rare environments.

Alleles↗

PubMed2003

An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine.

Arabinogalactan proteins (AGPs) are abundant plant proteoglycans implicated in plant growth and development. Here, we report the genetic characterization, partial purification and immunolocalization of a classical AGP (PtaAGP6, accession number AF101785) in loblolly pine (Pinus taeda L.). A PtaAGP6 full-length cDNA clone was expressed in bacteria. PtaAGP6 resembles tomato LeAGP-1 and Arabidopsis AtAGP17-19 in that they all possess a subdomain composed of basic amino acids. The accessibility of this domain in the glycoprotein makes it possible to label the PtaAGP6 epitopes on the cell surface or in the cell wall with polyclonal antibodies raised against this subdomain. The antibodies recognize the peptide of the basic subdomain and bind to the intact protein molecule. A soluble protein-containing fraction was purified from the differentiating xylem of pine trees by using beta-glucosyl Yariv reagent (beta-glcY) and was recognized by antibodies against the basic subdomain. Immunolocalization studies showed that the PtaAGP6 epitopes are restricted to a file of cells that just precede secondary cell wall thickening, suggesting roles in xylem differentiation and wood formation. The location of apparent labeling of the PtaAGP6 epitopes is separated from the location of lignin deposition. Multiple single nucleotide polymorphisms (SNPs) were detected in EST variants. Denaturing HPLC analysis of PCR products suggests that PtaAGP6 is encoded by a single gene. Mobility variation in denaturing gel electrophoresis was used to map PtaAGP6 SNPs to a site on linkage group 5.

Amino Acid Sequence↗

PubMed2001

Pollen pool heterogeneity in shortleaf pine, Pinus echinata Mill.

Pollen is the dominant vector of gamete exchange for most temperate tree species. Because pollen movement influences the creation, maintenance and erosion of genetic structure in adult populations, it is important to understand what factors influence the process of pollen movement. Isolation by distance in pollen donor populations can create highly structured pollen polls by increased sampling of local fathers. Extrinsic factors, such as the intervening vegetative structure and local pollen donor densities, can also influence the genetic composition of local pollen pools. Using paternally inherited chloroplast microsatellite markers, we examined the structure and diversity of pollen pools in Pinus echinata Mill. in southern Missouri, USA. Our analysis is based on a multivariate AMOVA analysis of stands ( approximately 1 ha; six per region) nested within regions (approximately 800 ha; four each). Significant multilocus structure of the pollen pool within regions (phiSR = 0.095), but not among regions (phiRT = 0.010), indicates that pollen movement is relatively restricted. Furthermore, the significant correlation between pairwise genetic and physical distances (Mantel correlation; rho = 0.32) provided support for the isolation by distance hypothesis. Our results indicated that availability of pollen donors did not affect diversity of the pollen pool, measured by the number of unique multilocus genotypes at each stand. However, pollen pool diversity was negatively associated with vegetative structure, measured as total forest tree density. Our findings indicated that on-going pollen movement within continuous forest is relatively restricted as a result of both isolation by distance and vegetative structure.

Chloroplasts↗

PubMedDate not supplied

Low genetic variation among killer whales (Orcinus orca) in the eastern north Pacific and genetic differentiation between foraging specialists.

Killer whales from the coastal waters off California through Alaska were compared for genetic variation at three nuclear DNA markers and sequenced for a total of 520 bp from the mitochondrial control region. Two putative sympatric populations that range throughout this region were compared. They can be distinguished by social and foraging behavior and are known as "residents" and "transients". We found low levels of variation within populations compared to other cetacean species. Comparisons between fish (resident) versus marine mammal (transient) foraging specialists indicated highly significant genetic differentiation at both nuclear and mitochondrial loci. This differentiation is at a level consistent with intraspecific variation. A comparison between two parapatric resident populations showed a small but fixed mtDNA haplotype difference. Together these data suggest low levels of genetic dispersal between foraging specialists and a pattern of genetic differentiation consistent with matrifocal population structure and small effective population size.

Alleles↗

PubMedDate not supplied

Population genetic structure and colonization sequence of Drosophila subobscura in the Canaries and Madeira Atlantic Islands as inferred by autosomal, sex-linked and mtDNA traits.

The genetic structure in Atlantic Islands and continental populations of Drosophila subobscura has been studied using autosomal and sex-linked allozymes and mitochondrial DNA (mtDNA) haplotypes. From the data it is deduced that whereas the Canary islands have long been isolated, the neighboring island of Madeira has been subjected to continuous migration from the mainland. In addition, sex-linked allozymes and mtDNA data show a large divergence between the geologically younger western islands of the Canarian Archipelago and the older central ones, finding strong founder effects in the former. Divergence rates of sex-linked and mitochondrial genes relative to autosomic loci several times higher than expected under neutrality have been explained by differential migration between sexes. The Canarian Archipelago colonization fits in well with a stepping-stone model of a directional east-west migration that parallels the geological origin of these Islands.

Animals↗

PubMed2005

Thirteen novel mutations in the factor VIII gene in the Nijmegen haemophilia A patient population.

The development of neutralising antibodies to factor VIII (FVIII) is a major complication of haemophilia A (HA) therapy. We aimed to construct an individual risk profile for the development of inhibitors in HA and started by screening for the causative mutation in our HA patient population. A total of 109 patients and 28 carriers were screened. The analysis revealed 38 different mutations in the FVIII gene, of which 13 have not been described on the Haemophilia A Mutation, Search, Test and Resource Site (HAMSTeRS). Twenty-five mutations have been reported previously and all except two had a similar phenotype to what has been described. Three novel mutations were associated with severe HA: one non-missense mutation, a small insertion in the A2 domain, and two missense mutations, a H256R mutation in the A1 domain and a L2025P substitution in the C1 domain. One novel mutation, Y156C, was associated with moderate HA. Nine novel mutations caused mild HA. The P130R, D167E and V278M mutations are located in the A1 domain. R439C, Y511H, A544G and Q645H in the A2 domain, L1758F in the A3 domain and a S2157R mutation in the C1 domain. In conclusion, the genotypic profile of our HA population was not different from others described and is suitable to study inhibitor formation.

Adolescent↗

PubMed2004

Phylogeography recapitulates topography: very fine-scale local endemism of a saproxylic 'giant' springtail at Tallaganda in the Great Dividing Range of south-east Australia.

Comparative phylogeography can reveal processes and historical events that shape the biodiversity of species and communities. As part of a comparative research program, the phylogeography of a new, endemic Australian genus and species of log-dependent (saproxylic) collembola was investigated using mitochondrial sequences, allozymes and anonymous single-copy nuclear markers. We found the genetic structure of the species corresponds with five a priori microbiogeographical regions, with population subdivision at various depths owing to palaeoclimatic influences. Closely related mtDNA haplotypes are codistributed within a single region or occur in adjacent regions, nuclear allele frequencies are more similar among more proximate populations, and interpopulation migration is rare. Based on mtDNA divergence, a late Miocene-late Pliocene coalescence is likely. The present-day distribution of genetic diversity seems to have been impacted by three major climatic events: Pliocene cooling and drying (2.5-7 million years before present, Mybp), early Pleistocene wet-dry oscillations (c. 1.2 Mybp) and the more recent glacial-interglacial cycles that have characterized the latter part of the Quaternary (<0.4 Mybp).

Animals↗

PubMed2005

Phylogeography of marine mutualists: parallel patterns of genetic structure between obligate goby and shrimp partners.

The survival of many organisms depends on interspecific, mutualistic interactions. Hence, it is important to assess the phylogeography of multiple mutualistic species simultaneously to gain insight into how their metapopulations persist, spread and recover from disturbance. Consequently, we sequenced mitochondrial DNA (cytochrome b) from a gobiid fish (Ctenogobiops feroculus) and its mutualistic partner, an alpheid snapping shrimp (Alpheus djeddensis). These obligate mutualists are common in shallow coral reef lagoons, and we collected individuals from 11 Indo-Pacific islands that were likely exposed to different disturbance histories due to sea level fluctuations associated with glaciation events [geological studies indicate that eastern oceanic islands (Cook Islands, French Polynesia) were more disturbed than western continental plate islands that have deeper, more extensive lagoons (Okinawa, Fiji)]. Both phylogenetic and population genetic analyses indicated that gobies from Okinawa and Fiji were genetically distinct both from each other and those in the Cook Islands and French Polynesia. Shrimp, by contrast, grouped into two distinct genetic groups that showed no geographic structure. Restricting the analysis to one clade of shrimp, which contained two-thirds of the individuals, showed that these shrimp had very similar phylogeographical structure to the gobies. Mismatch distributions demonstrated that both gobies and shrimp experienced a recent, rapid population expansion into French Polynesia. Finally, nucleotide and haplotype diversities per sample location were significantly correlated between mutualists and tended to be higher on western continental than eastern oceanic islands. Our results suggest that these mutualists recovered from a major disturbance by colonizing South Pacific islands in synchrony.

Animals↗

PubMed2005

Pan-European phylogeography of the aquatic snail Theodoxus fluviatilis (Gastropoda: Neritidae).

Investigating the geographical distribution of genetic lineages within species is critical to our understanding of how species evolve. As many species inhabit large and complex ranges, it is important that phylogeographical research take into account the entire range of widespread species to clarify how myriad extrinsic variables have affected their evolutionary history. Using phylogenetic, nested clade, and mismatch distribution analyses on a portion of the mitochondrial COI gene, I demonstrate that the wide-ranging freshwater snail Theodoxus fluviatilis possesses in parallel many of the phylogeographical patterns seen in less widespread freshwater species of Europe. Fragmentary forces play a major part in structuring the range of this species, with 12 of 14 geographically structured nested clades displaying a distribution consistent with fragmentation or restricted dispersal. Certain regions of southern Europe harbour the majority of genetic diversity (total haplotype diversity, H = 0.87), particularly Italy (H = 0.87) and areas surrounding the Black Sea (H = 0.81). Post-Pleistocene range expansion is pronounced, with the majority of northern European populations (95% of sample sites) having arisen from northern Italian individuals that initially colonized northern Germany. Additionally, two highly divergent haplotype lineages present in northern Germany imply that there were at least two postglacial recolonization routes. Estuaries may also provide a means of dispersal given that no genetic differentiation was found between estuarine populations and neighbouring freshwater populations. Taken together, these data reveal a species with a complex genetic history resulting from the fragmentary effects of European geology as well as continuous and discrete range expansion related to their aquatic biology.

Animals↗