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PubMed2006

Population dynamics and gene flow of Helicoverpa armigera (Lepidoptera: Noctuidae) on cotton and grain crops in the Murrumbidgee Valley, Australia.

The population dynamics of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in the Murrumbidgee Valley, Australia, has been characterized using five highly variable microsatellite loci. In the 2001-2002 growing season, there were very high levels of migration into the Murrumbidgee Valley with no detectable genetic structuring, consistent with previous analyses on a national scale. By contrast, there was significant genetic structuring over the 2002-2003 growing season, with three distinct genetic types detected. The first type corresponded to the first two generations and was derived from local individuals emerging from diapause and their progeny. The second genetic type corresponded to generation 3 and resulted from substantial immigration into the region. There was another genetic shift in generation 4, which accounts for the third genetic type of the season. This genetic shift occurred despite low levels of immigration. During the third generation of the 2002-2003 growing season, different population dynamics was characterized for H. armigera on maize, Zea mays L., and cotton Gossipium hirsutum L. Populations on cotton tended to cycle independently with very little immigration from outside the region or from maize within the region. Maize acted as a major sink for immigrants from cotton and from outside the region. If resistance were to develop on cotton under these circumstances, susceptible individuals from maize or from other regions would not dilute this resistance. In addition, resistance is likely to be transferred to maize and be perpetuated until diapause, from where it may reemerge next season. If low levels of immigration were to occur on transgenic cotton, this may undermine the effectiveness of refugia, especially noncotton refugia.

Animals↗

PubMed2005

Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity.

Cyclotella meneghiniana Kützing is one of the most commonly found and intensively studied freshwater diatom species. However, it is considered taxonomically problematic because of its unusually wide ecological range and large frustule ultrastructural variation. As part of a study of morphological and genetic variation in this morphospecies, we surveyed nucleotide variation in the hypervariable D1/D2 regions of the 28S rDNA, in the ribosomal internal transcribed spacer region (containing ITS1, the 5.8S rDNA and ITS2) and in the 18S rDNA in a collection of 20 sympatric strains. High genetic variability and strong indications of genetic structure among the Cyclotella meneghiniana strains were found. Representatives of four genetically distinct--apparently reproductively isolated--groups were revealed among them. The random distribution of ITS variation within these four groups indicated that the genetic structure in Cyclotella meneghiniana can probably be explained by the presence of cryptic sexual species rather than by the lack of allogamous sexual reproduction. The morphological features traditionally used for species identification in this group cannot distinguish these putative cryptic species.

Animals↗

PubMed2000

The genetic legacy of the Quaternary ice ages.

Global climate has fluctuated greatly during the past three million years, leading to the recent major ice ages. An inescapable consequence for most living organisms is great changes in their distribution, which are expressed differently in boreal, temperate and tropical zones. Such range changes can be expected to have genetic consequences, and the advent of DNA technology provides most suitable markers to examine these. Several good data sets are now available, which provide tests of expectations, insights into species colonization and unexpected genetic subdivision and mixture of species. The genetic structure of human populations may be viewed in the same context. The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help our understanding of how organisms were so affected.

Animals↗

PubMed1999

Y-chromosome specific YCAII, DYS19 and YAP polymorphisms in human populations: a comparative study.

Two hypervariable Y-specific markers, the YCAII and DYS19 STRs, and the more stable Y Alu Polymorphism (YAP) have been analysed in about 1400 individuals of 21 different populations, mainly from Europe but also from the Middle East, Africa and Asia. On the basis of the frequency distributions of these three Y-markers we compare, using different statistical analyses, their power in detecting population genetic structure and in distinguishing closely related groups. The pattern of populations' genetic affinities inferred from the three markers considered altogether suggests a strong genetic structure that, with a few exceptions, broadly corresponds to the linguistic relatedness and/or geographic location of the sampled populations.

Alleles↗

PubMed2004

Training HMM structure with genetic algorithm for biological sequence analysis.

SUMMARY: Hidden Markov models (HMMs) are widely used for biological sequence analysis because of their ability to incorporate biological information in their structure. An automatic means of optimizing the structure of HMMs would be highly desirable. However, this raises two important issues; first, the new HMMs should be biologically interpretable, and second, we need to control the complexity of the HMM so that it has good generalization performance on unseen sequences. In this paper, we explore the possibility of using a genetic algorithm (GA) for optimizing the HMM structure. GAs are sufficiently flexible to allow incorporation of other techniques such as Baum-Welch training within their evolutionary cycle. Furthermore, operators that alter the structure of HMMs can be designed to favour interpretable and simple structures. In this paper, a training strategy using GAs is proposed, and it is tested on finding HMM structures for the promoter and coding region of the bacterium Campylobacter jejuni. The proposed GA for hidden Markov models (GA-HMM) allows, HMMs with different numbers of states to evolve. To prevent over-fitting, a separate dataset is used for comparing the performance of the HMMs to that used for the Baum-Welch training. The GA-HMM was capable of finding an HMM comparable to a hand-coded HMM designed for the same task, which has been published previously.

Algorithms↗

PubMed1999

Structural and genetic studies of the proliferation disrupter genes of Drosophila simulans and D. melanogaster.

To examine whether structural and functional differences exist in the proliferation disrupter (prod) genes between Drosophila simulans and D. melanogaster, we analyzed and compared both genes. The exon-intron structure of the prod genes was found to be the same--three exons were interrupted by two introns, although a previous report suggested that only one intron existed in D. melanogaster. The prod genes of D. simulans and D. melanogaster both turn out to encode 346 amino acids, not 301 as previously reported for D. melanogaster. The numbers of nucleotide substitutions in the prod genes was 0.0747 +/- 0.0180 per synonymous site and 0.0116 +/- 0.0039 per replacement site, both comparable to those previously known for homologous genes between D. simulans and D. melanogaster. Genetic analysis demonstrated that D. simulans PROD can compensate for a deficiency of D. melanogaster PROD in hybrids. The PRODs of D. simulans and D. melanogaster presumably share the same function and a conserved working mechanism. The prod gene showed no significant interaction with the lethality of the male hybrid between these species.

Amino Acid Sequence↗

PubMed2005

Panmixia in the European eel: a matter of time...

The European eel (Anguilla anguilla L.) has been a prime example of the panmixia paradigm because of its extraordinary adaptation to the North Atlantic gyral system, semelparous spawning in the Sargasso Sea and long trans-oceanic migration. Recently, this view was challenged by the suggestion of a genetic structure characterized by an isolation-by-distance (IBD) pattern. This is only likely if spawning subpopulations are spatially and/or temporally separated, followed by non-random larval dispersal. A limitation of previous genetic work on eels is the lack of replication over time to test for temporal stability of genetic structure. Here, we hypothesize that temporal genetic variation plays a significant role in explaining the spatial structure reported earlier for this species. We tested this by increasing the texture of geographical sampling and by including temporal replicates. Overall genetic differentiation among samples was low, highly significant and comparable with earlier studies (FST = 0.0014; p < 0.01). On the other hand, and in sharp contrast with current understandings, hierarchical analyses revealed no significant inter-location genetic heterogeneity and hence no IBD. Instead, genetic variation among temporal samples within sites clearly exceeded the geographical component. Our results provide support for the panmixia hypothesis and emphasize the importance of temporal replication when assessing population structure of marine fish species.

Anguilla↗

PubMed2006

Aminopropyltransferases: function, structure and genetics.

Aminopropyltransferases use decarboxylated S-adenosylmethionine as an aminopropyl donor and an amine acceptor to form polyamines. This review covers their structure, mechanism of action, inhibition, regulation and function. The best known aminopropyltransferases are spermidine synthase and spermine synthase but other members of this family including an N(1)-aminopropylagmatine synthase have been characterized. Spermidine synthase is an essential gene in eukaryotes and is very widely distributed. Key regions in the active site, which are very highly conserved, were identified by structural studies with spermidine synthase from Thermotoga maritima bound to S-adenosyl-1,8-diamino-3-thiooctane, a multisubstrate analog inhibitor. A general mechanism for catalysis by aminopropyltransferases can be proposed based on these studies. Spermine synthase is less widely distributed and is not essential for growth in yeast. However, Gy mice lacking spermine synthase have multiple symptoms including a profound growth retardation, sterility, deafness, neurological abnormalities and a propensity to sudden death, which can all be prevented by transgenic expression of spermine synthase. A large reduction in spermine synthase in human males due to a splice site variant causes Snyder-Robinson syndrome with mental retardation, hypotonia and skeletal abnormalities.

Amines↗

PubMed2005

ISSR markers show differentiation among Italian populations of Asparagus acutifolius L.

BACKGROUND: Asparagus acutifolius L. is a dioecious and native plant species, widely distributed in the Mediterranean Basin. It is known for its fine flavour and could represent an important resource for cultivation programs in desert areas. Few molecular studies have been performed on this species. In the present paper, the ISSR technique was employed to study genetic diversity in Italian A. acutifolius. RESULTS: Twenty-three primers produced a total of 228 polymorphic fragments used to evaluate genetic variation. FST (0.4561) and Theta B (0.4776) values indicate a wide genetic variation among the samples examined. The distance UPGMA tree grouped together the genotypes strictly according to their geographical origin, showing that each sample is genetically structured and can be considered a distinct population. AMOVA analysis further confirmed genetic structuring of the populations. Population-specific fragments were also detected. CONCLUSION: The results suggest that ISSR markers are useful in distinguishing the populations of A. acutifolius according to geographical origin, and confirm the importance of genetic studies for designing germplasm conservation strategies.

Asparagus Plant↗

PubMed2003

The influence of history and contemporary stream hydrology on the evolution of genetic diversity within species: an examination of microsatellite DNA variation in bull trout, Salvelinus confluentus (Pisces: Salmonidae).

An understanding of the relative roles of historical and contemporary factors in structuring genetic variation is a fundamental, but understudied aspect of geographic variation. We examined geographic variation in microsatellite DNA allele frequencies in bull trout (Salvelinus confluentus, Salmonidae) to test hypotheses concerning the relative roles of postglacial dispersal (historical) and current landscape features (contemporary) in structuring genetic variability and population differentiation. Bull trout exhibit relatively low intrapopulation microsatellite variation (average of 1.9 alleles per locus, average He = 0.24), but high levels of interpopulation divergence (F(ST) = 0.39). We found evidence of historical influences on microsatellite variation in the form of a decrease in the number of alleles and heterozygosities in populations on the periphery of the range relative to populations closer to putative glacial refugia. In addition, one region of British Columbia that was colonized later during deglaciation and by more indirect watershed connections showed less developed and more variable patterns of isolation by distance than a similar region colonized earlier and more directly from refugia. Current spatial and drainage interconnectedness among sites and the presence of migration barriers (falls and cascades) within individual streams were found to be important contemporary factors influencing historical patterns of genetic variability and interpopulation divergence. Our work illustrates the limited utility of equilibrium models to delineate population structure and patterns of genetic diversity in recently founded populations or those inhabiting highly heterogeneous environments, and it highlights the need for approaches incorporating a landscape context for population divergence. Substantial microsatellite DNA divergence among bull trout populations may also signal divergence in traits important to population persistence in specific environments.

Alberta↗

PubMed1975

Properties of the imidazolylacetolphosphate aminotransferase produced in a mutant demonstrating no apparent genetic involvement of the structural gene.

Genetic studies with strain hisBH22 of Salmonella typhimurium indicate it contains a deletion within the histidine operon involving part of the hisH gene and all of the hisB gene, but not extending into the adjacent hisC gene which is adjacent to hisB. However, the specific activity of the hisC product, imidazolylacetolphosphate aminotransferase (EC 2.6.1.9), in this strain is only 10 to 15% of that found in extracts from other mutants with a normal hisC gene. We have examined the rate of aminotransferase synthesis in this mutant and we find that the rate of synthesis of aminotransferase activity is low in mutant hisBH22, but the rate increases as the temperature of growth is lowered from 37 to 23 C. The low rate of enzyme accumulation is not due to holoenzyme instability at 37 C but instead is due to apoenzyme instability at this temperature. By transducing the hisBH22 marker into a pyridoxine auxotroph and derepressing the histidine operon under conditions where the intracellular concentration of pyridoxal phosphate would be expected to be low, we were able to demonstrate significant apoenzyme production only at the lower temperature. We suggest that the explanation for low aminotransferase specific activity at 37 C is due to the presence of reduced numbers of catalytically active units caused by normal production of an unstable mutant apoenzyme with only approximately 15% of the molecules being activated to holoenzyme. The holoenzyme from strain hisBH22 is stable during growth of this strain at 37 C.

Coliphages↗

PubMed2024

A genetic atlas for the butterflies of continental Canada and United States.

Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.

Animals↗

PubMed1993

The cytochrome b-558 molecules involved in the fibroblast and polymorphonuclear leucocyte superoxide-generating NADPH oxidase systems are structurally and genetically distinct.

We have demonstrated that human fibroblasts can release O2-. radicals by an NADPH oxidase system that appears to be functionally similar to the phagocytic system. Further analysis of these systems, however, with respect to the low-potential b-type cytochromes involved suggests that these two O2-.-generating systems are not structurally identical. Immunoblot analysis of fibroblast membranes with six different antibodies directed against both subunits of human neutrophil cytochrome b-558 indicated that the b-type cytochrome molecules involved in these systems were not identical. None of these anti-(neutrophil cytochrome b) antibodies recognized a similar cytochrome in fibroblast membranes, suggesting that the two cytochrome species are immunologically distinct. In addition, fibroblasts obtained from a patient suffering from X-linked chronic granulomatous disease (CGD) had a normal cytochrome b-558 content compared with control fibroblast membranes, whereas the cytochrome b-558 concentration in polymorphonuclear leucocytes (PMNs) from this patient was decreased to 10% of that found in PMNs from healthy controls. Likewise, the stimulated O2-. release in PMNs from this patient was less than 10% of that in control PMNs, whereas the fibroblasts showed stimulated O2-.-release rates that were indistinguishable from those of fibroblasts obtained from healthy persons. Since the genetic mutation responsible for this type of CGD results in the absence of cytochrome b-558 in PMNs, fibroblasts should be affected in the same way if both cytochrome species were identical. These results suggest therefore that the low-potential b-type cytochromes in PMNs and fibroblasts are structurally and genetically distinct.

Antibodies↗

PubMed2004

Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle.

The East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long-lived, fecund snapper species that is distributed throughout the East Indies and Indo-Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67-0.82), as was intraspecific sequence divergence (range 0-5.8%). F(ST) between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; F(ST) was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents.

Analysis of Variance↗

PubMed2025

Population stratification in Northern shrimp (Pandalus borealis) off Iceland evident from RADseq analysis.

The northern shrimp Pandalus borealis (ice. Stóri kampalampi) is a North Atlantic crustacean of significant commercial interest which has been harvested consistently in Icelandic waters since 1936. In Icelandic waters, the length at which this protandrous species transitions from male to female differs between the inshore and offshore populations, suggesting a biologically meaningful stratification which may or may not be plastic. Using reduced representative genomes assembled from RADseq data, sampled from 96 individuals collected at two time points (2018 and 2021), we compare the level of genetic structure across a gradient extending out of Skjálfandi bay, north Iceland. These data are compared to samples from a far offshore site, some 65 km out from the bay, as well as another inshore fjord in Arnarfjörður, in northwestern Iceland. Since 1999, no harvesting of inshore populations of P. borealis in Skjálfandi has been allowed due to stock decline, but harvesting of offshore stocks has continued. Uncertainty surrounding the extent of structure between the in- and offshore aggregations has remained. Here we report distinct genetic structure defining the inshore and offshore populations of northern shrimp, but find significant admixture between the two. Most importantly, we see that genetically inshore populations of northern shrimp extend far outside the harvest boundaries of inshore shrimp, and offshore individuals may exhibit punctuated migration into the inshore areas.

Animals↗

PubMed2006

Palaeopolyploidy, spatial structure and conservation genetics of the narrow steppe plant Vella pseudocytisus subsp. paui (Vellinae, Cruciferae).

BACKGROUND AND AIMS: Vella pseudocytisus subsp. paui (Cruciferae) is a narrow endemic plant to the Teruel province (eastern Spain), which is listed in the National Catalogue of Endangered Species. Two distinct ploidy levels (diploid, 2n = 34, and tetraploid, 2n = 68) have been reported for this taxon that belongs to the core subtribe Vellinae, a western Mediterranean group of shrubby taxa with a chromosome base number of x = 17. Allozyme and AFLP analyses were conducted (a) to test for the ploidy and putative palaeo-allopolyploid origin of this taxon, (b) to explore levels of genetic diversity and spatial structure of its populations, and (c) to address in-situ and ex-situ strategies for its conservation. METHODS: Six populations that covered the entire geographical range of this taxon were sampled and examined for 19 allozyme loci and three AFLP primer pair combinations. In addition, the gametic progenies of five individuals were analysed for two allozyme loci that showed fixed heterozygosity. KEY RESULTS: Multiple banded allozyme profiles for most of the surveyed loci indicated the polyploidy of this taxon. Co-inherited fixed heterozygous patterns were exhibited by the gametophytic tissues of the mother plants. Both allozyme and AFLP markers detected high levels of genetic diversity, and a strong micro-spatial genetic structure was recovered from AFLP phenetic analyses and Mantel correlograms. CONCLUSIONS: Allozyme data support the hypothesis of an allotetraploid origin of Vella pseudocytisus subsp. paui that could be representative of other taxa of the core Vellinae group. AFLP data distinguished three geographically distinct groups with no genetic interaction among them. Allotetraploidy and outcrossing reproduction have probably contributed to maintenance of high levels of genetic variability of the populations, whereas habitat fragmentation may have enhanced the high genetic isolation observed among groups. In-situ microgenetic reserves and a selective sampling of germplasm stocks for ex-situ conservation of this taxon are proposed.

Brassicaceae↗

PubMed2025

Habitat Specialisation Impacts Clownfish Demographic Resilience to Pleistocene Sea-Level Fluctuations.

Habitat fragmentation and loss are key threats to biodiversity, yet their impacts on marine species remain poorly understood. Clownfishes, which rely on sea anemones for shelter and reproduction, provide an interesting model to explore how ecological specialisation mediates species responses to habitat perturbations. We used whole-genome data from 382 individuals across 10 species with varying host specialisations to reconstruct demographic histories and infer spatial genetic structure to assess the impact of Pleistocene sea-level fluctuations. Generalist species, associated with multiple hosts, maintained stable effective population sizes () and population connectivity during habitat fragmentation, reflecting resilience to environmental instability. In contrast, specialists experienced severedeclines and genetic structuring, driven by their dependence on specific hosts, without signs of population recovery following habitat reconnection. Spatial genomic analyses identified the Indonesian Through-Flow as a key dispersal corridor and the Coral Triangle as a critical hub of genetic diversity, while continental shelves and extensive open ocean regions appeared as barriers to gene flow. Our findings reveal how host specialisation shapes clownfish population dynamics, emphasising the importance of incorporating ecological dependencies into conservation assessments and deepening our understanding of species responses to ecological constraints and environmental changes over evolutionary timescales.

Animals↗

PubMed1999

STR polymorphisms in the population of the island of Hvar.

The aim of this study is to analyze short tandem repeat (STR) variation using data on 9 loci (D3S1358, VWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) from the subpopulations of 6 villages on the island of Hvar, Croatia. The STR data help us to analyze the genetic structure of Hvar. The analysis of STR data in this study indicated genetic homogeneity among the village subpopulations on Hvar and the lack of the so-called east-west dichotomy, which had been indicated by some previous multidisciplinary anthropological studies. The observed value of GST (0.030) is most probably a consequence of high STR mutation rates, which produce a high level of within-group (village) diversity relative to total diversity of the population. The validity of STR markers in assessing genetic structure of small populations and especially in determining the relationships among closely related and reproductively isolated groups remains to be further evaluated.

Chi-Square Distribution↗