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At least 1,315 records · Page 73Linked to original sources
PubMed2005

Chloroplast DNA variation of Quercus rubra L. in North America and comparison with other Fagaceae.

Quercus rubra is one of the most important timber and ornamental tree species from eastern North America. It is a widespread species growing under variable ecological conditions. Chloroplast DNA variation was studied by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) in 290 individuals from 66 populations sampled throughout the natural range. A total of 12 haplotypes were detected, with one found in 75% of the trees. Population differentiation is relatively low (G(ST) = 0.46), even when similarities between haplotypes are taken into account (N(ST) = 0.50), pointing to a weak phylogeographical structure. Furthermore, no spatial structure of genetic diversity could be detected. The genetic differentiation increased northwards, reflecting the postglacial history of Q. rubra. The unusual aspect of this study was the low level of chloroplast DNA genetic differentiation in Q. rubra compared to that typically observed in other oak species. Palynological evidence indicates that during the last glacial maximum, Q. rubra had one major distribution range with populations located relatively far to the north, resulting in only modest movement northwards when climate improved, whereas European white oaks were largely restricted to the southern European peninsulas and experienced extensive movements during the postglacial period. The contrasted geographical features and levels of tree species richness of both continents might further explain why congeneric species sharing similar life history traits have genetic structures that are so different.

DNA, Chloroplast↗
PubMedDate not supplied

[Protein polymorphism in the crossbred progeny of Simmental and Red-and-White Holsteins].

The analysis of the genetic structure at 12 genetic-biochemical systems of pure parental breeds and their mixed offspring was carried out. The genetic structure of the mixed offspring was also investigated in relation with their differences in milk productivity. Locus-specific peculiarities of reorganization of the gene pool in the process of obtaining mixed offspring were described. Some genetic-biochemical systems involved in differentiation of groups of animals with respect to characteristics of milk production were revealed.

Alleles↗
PubMed2003

Introgression patterns in the mosaic hybrid zone between Mytilus edulis and M. galloprovincialis.

Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis, using three length-polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient from M. galloprovincialis on the Iberian Peninsula to M. edulis populations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical of M. galloprovincialis first decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantly M. edulis-like and M. galloprovincialis-like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre- or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory 'short-cut' connecting M. edulis-like populations of the Charente patch to an external M. edulis population in Normandy and thought to reflect artificial transfer of spat for aquaculture.

Alleles↗
PubMed1998

Phylogeography of the freshwater fish, Mogurnda adspersa, in streams of northeastern Queensland, Australia: evidence for altered drainage patterns.

A phylogeographic survey was used to elucidate the relative roles of historical processes and contemporary gene flow in structuring the genetic pattern observed with Mogurnda adspersa. This species of freshwater fish is found in the rivers and streams of the northeastern highlands of Queensland, Australia. Specifically, this project focused on populations in the Tully and Herbert Rivers in the Atherton Tablelands. Sequence analysis indicated that three distinct clades exist in the headwaters of the Tully River. The population sampled from one of the Tully River streams (Cheetah Creek) contained haplotypes that displayed approximately 3.4% sequence divergence from other haplotypes detected in this river. Furthermore, these haplotypes formed part of the clade which exists throughout not only the Herbert River but other surrounding drainages in the area. These results support the hypothesis that the current genetic structure is strongly affected by changes in drainage patterns due to geomorphological processes that occurred in the recent past.

Animals↗
PubMed2006

Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants.

We have examined the global population genetic structure of Haemonchus contortus. The genetic variability was studied using both amplified fragment length polymorphism (AFLP) and nad4 sequences of the mitochondrial genome. To examine the performance and information content of the two different marker systems, comparative assessment of population genetic diversity was undertaken in 19 isolates of H. contortus, a parasitic nematode of small ruminants. A total of 150 individual adult worms representing 14 countries from all inhabited continents were analysed. Altogether 1,429 informative AFLP markers were generated using four different primer combinations. Also, the genetic variation was high, which agrees with results from previous AFLP studies of nematode parasites of livestock. The genetic structure was high, indicating limited gene flow between the different isolates and populations from each continent mostly formed monophyletic groups in the phylogenetic analysis. However, for isolates representing Australia, Greece and one laboratory strain that originated from South Africa (WRS), there was no clear genetic relationship between the isolates and the distance between their geographical origins. Basically the same pattern was observed for the mitochondrial marker, although the phylogenetic analysis was less resolved than for AFLP. In contrast with previous findings on the population genetic structure of H. contortus, the calculation of population structure gave high values (Nst=0.59). The strong structure was present also for the four Swedish isolates (Nst=0.16) representing a small geographical area.

Animals↗
PubMed2006

Comparative phylogeography of three codistributed stomatopods: origins and timing of regional lineage diversification in the Coral Triangle.

The Indonesian-Australian Archipelago is the center of the world's marine biodiversity. Although many biogeographers have suggested that this region is a "center of origin," criticism of this theory has focused on the absence of processes promoting lineage diversification in the center. In this study we compare patterns of phylogeographic structure and gene flow in three codistributed, ecologically similar Indo-West Pacific stomatopod (mantis shrimp) species. All three taxa show evidence for limited gene flow across the Maluku Sea with deep genetic breaks between populations from Papua and Northern Indonesia, suggesting that limited water transport across the Maluku Sea may limit larval dispersal and gene flow across this region. All three taxa also show moderate to strong genetic structure between populations from Northern and Southern Indonesia, indicating limited gene flow across the Flores and Java Seas. Despite the similarities in phylogeographic structure, results indicate varied ages of the genetic discontinuities, ranging from the middle Pleistocene to the Pliocene. Concordance of genetic structure across multiple taxa combined with temporal discordance suggests that regional genetic structures have arisen from the action of common physical processes operating over extended time periods. The presence in all three species of both intraspecific genetic structure as well as deeply divergent lineages that likely represent cryptic species suggests that these processes may promote lineage diversification within the Indonesian-Australian Archipelago, providing a potential mechanism for the center of origin. Efforts to conserve biodiversity in the Coral Triangle should work to preserve both existing biodiversity as well as the processes creating the biodiversity.

Animals↗
PubMed1981

[Lambda H-lambda T 80 hybrid study of the DNA structural gene region in lambda and phi 80 phages].

Hybrids lambda H lambda T80 are formed due to recombination of the phage lambda att80 and phi 80 prophage partially deleted in the region of structural genes. Genetic structure of 22 independently isolated lambda H lambda T80 hybrids was determined by the restriction method and it was shown that recombination took place in the genes A, C, D and H. The frequencies of hybrid formation diminish from 1.10(-3) to 4.10(-5) for this gene order, which suggests that the polar divergence of nucleotide sequencies in the region of structural genes exists. It was found that formation of hybrids with recombination in the region of "weak" homology (gene H) was possible only when the region of "strong" homology was present in the deleted phi 80 prophage to initiate recombination.

Bacteriophage lambda↗
PubMed1991

Complement.

The complement system mediates a wide range of important biological functions. The use of modern techniques in protein chemistry and molecular biology has greatly facilitated our understanding of the interactions between the fluid phase and cell-bound components of the system. Structural and genetic analysis has shown that while many of these components are polymorphic, there are major similarities between many of the proteins serving enzymatic and regulatory roles in both the alternative and classical pathways. The regulation of complement activation and Class III genes, on chromosomes 1 and 6 respectively, encode nine of the major proteins in the system. The genetic basis of C4 and C3 polymorphisms is now well established, and further study may reveal functional differences between polymorphic variants of other components. The study of individuals with either genetic or acquired deficiencies of complement proteins and receptors has provided insight into the function of these components, leukocyte adherence deficiency (LAD) providing the best example. An appreciation of the genetics, structure and functions of the regulatory proteins decay-accelerating factor (DAF) and homologous restriction factor has enhanced our understanding of the pathogenesis of paroxysmal nocturnal haemoglobinuria. The full importance of CD59 glycoprotein, the newest member of the complement family, remains to be determined.

Autoimmune Diseases↗
PubMed1994

Structure-function correlates of autoantibodies to nucleic acids. Lessons from immunochemical, genetic and structural studies.

Nucleic acid binding autoantibodies are the hallmark of the human autoimmune disease, systemic lupus erythematosus (SLE) and are also prevalent in mouse models of this disease. The immunologic stimuli for the production of these antibodies as well as their pathogenic mechanisms are not well understood. However, extensive immunochemical and genetic studies, together with initial crystallographic analysis and computer modeling, have suggested several structure-function correlates which will form the basis for future research. The anti-DNA and anti-RNA autoantibodies comprise a continuous spectrum of specificities in which a delicate balance exists between the binding to the sugar-phosphate backbone and the interactions with the heterocyclic bases of the nucleic acid. Prominent in these interactions are the products of specific V-region immunoglobulin genes, some of which appear to be uniquely suitable for nucleic acid binding. Other structural elements encoded by D minigenes, N sequences and somatic mutations, help to increase the affinity of the binding interaction, and may also increase the repertoire of nucleic acid binding antibodies by combining with a relatively large number of additional V-gene products. Initial crystallographic analyses of anti-DNA antibodies indicate some fundamental differences in the structure and shape of ssDNA and dsDNA antibody combining sites. However, they also suggest a considerable degree of flexibility of both antibody and antigen, which is induced by their binding interaction.

Amino Acid Sequence↗
PubMed2005

Inter- and intra-specific variation among five Erythroxylum taxa assessed by AFLP.

BACKGROUND: and Aims The four cultivated Erythroxylum taxa (E. coca var. coca, E. novogranatense var. novogranatense, E. coca var. ipadu and E. novogranatense var. truxillense) are indigenous to the Andean region of South America and have been cultivated for folk-medicine and, within the last century, for illicit cocaine production. The objective of this research was to assess the structure of genetic diversity within and among the four cultivated alkaloid-bearing taxa of Erythroxylum in the living collection at Beltsville Agricultural Research Center. METHODS: Amplified fragment length polymorphism (AFLP) fingerprinting was performed in 86 Erythroxylum accessions using a capillary genotyping system. Cluster analysis, multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) were used to assess the pattern and level of genetic variation among and within the taxa. KEY RESULTS: A clear distinction was revealed between E. coca and E. novogranatense. At the intra-specific level, significant differentiation was observed between E. c. var. coca and E. c. var. ipadu, but the differentiation between E. n. var. novogranatense and E. n. var. truxillense was negligible. Erythroxylum c. var. ipadu had a significantly lower amount of diversity than the E. c. var. coca and is genetically different from the E. c. var. ipadu currently under cultivation in Colombia, South America. CONCLUSIONS: There is a heterogeneous genetic structure among the cultivated Erythroxylum taxa where E. coca and E. novogranatense are two independent species. Erythroxylum coca var. coca is most likely the ancestral taxon of E. c. var. ipadu and a founder effect may have occurred as E. c. var. ipadu moved from the eastern Andes in Peru and Bolivia into the lowland Amazonian basin. There is an indication of artificial hybridization in coca grown in Colombia.

Coca↗
PubMed1977

Structural and genetic studies on chicken 7S immunoglobulin allotypes. III. Proposed nomenclature for the CS-1 gene alleles.

A survey of 47 inbred or partially inbred chicken lines derived from five sources in the United States and Europe revealed considerable genetic polymorphism in the structural gene (CS-1) responsible for the production of the predominant chicken 7S Ig heavy chain. A minimum of 10 alleles of the CS-1 gene were detected as unique combinations or phenogroups of CS-1 specificities. A system of nomenclature for CS-1 alleles was developed and six homozygous lines were designated as prototype lines. The remaining four CS-1 alleles occurred only in lines that were polymorphic for 7S Ig allotypic specificities.

Alleles↗
PubMed1998

How organisms do the right thing: The attractor hypothesis.

Neo-Darwinian theory is highly successful at explaining the emergence of adaptive traits over successive generations. However, there are reasons to doubt its efficacy in explaining the observed, impressively detailed adaptive responses of organisms to day-to-day changes in their surroundings. Also, the theory lacks a clear mechanism to account for both plasticity and canalization. In effect, there is a growing sentiment that the neo-Darwinian paradigm is incomplete, that something more than genetic structure, mutation, genetic drift, and the action of natural selection is required to explain organismal behavior. In this paper we extend the view of organisms as complex self-organizing entities by arguing that basic physical laws, coupled with the acquisitive nature of organisms, makes adaptation all but tautological. That is, much adaptation is an unavoidable emergent property of organisms' complexity and, to some a significant degree, occurs quite independently of genomic changes wrought by natural selection. For reasons that will become obvious, we refer to this assertion as the attractor hypothesis. The arguments also clarify the concept of "adaptation." Adaptation across generations, by natural selection, equates to the (game theoretic) maximization of fitness (the success with which one individual produces more individuals), while self-organizing based adaptation, within generations, equates to energetic efficiency and the matching of intake and biosynthesis to need. Finally, we discuss implications of the attractor hypothesis for a wide variety of genetical and physiological phenomena, including genetic architecture, directed mutation, genetic imprinting, paramutation, hormesis, plasticity, optimality theory, genotype-phenotype linkage and puncuated equilibrium, and present suggestions for tests of the hypothesis. (c) 1998 American Institute of Physics.

Journal Article↗
PubMed2006

When invaders meet locally adapted types: rapid moulding of hybrid zones between sculpins (Cottus, Pisces) in the Rhine system.

Hybrid zones are commonly studied to dissect the processes that drive divergence among lineages, which have incomplete barriers of reproduction. Most hybrid zones have existed for an extended time making inferences on the initial mode of formation difficult. It is a priori unclear how fast a nascent hybrid zone would form as a response to endogenous and exogenous factors. We have studied several hybrid zones between two lineages of sculpins (Cottus spp.), which emerged due to a recent range expansion of one of the lineages along the river Rhine in the early 1990s. Applying a dense sampling across two contact areas and using a highly informative set of 45 microsatellite markers we found pronounced genetic structure. Steep genetic clines suggest that strong selective forces have shaped the respective hybrid zones from the beginning. We find that the zones are coupled to ecological transitions from small streams to larger rivers. The width of these zones is much smaller than estimates of annual individual dispersal distances, as estimated outside of the hybrid zones. The pattern is apparently not strongly affected by pre- or postzygotic reproductive isolation because numerous backcross hybrids occur within the zones. This suggests that strong natural selection acts against immigrant genotypes. The study exemplifies how local adaptation can play a key role in preventing admixture in dependence of the ecological context.

Adaptation, Physiological↗
PubMed2022

A Multitrait Locus Regulates Sarbecovirus Pathogenesis.

Infectious diseases have shaped the human population genetic structure, and genetic variation influences the susceptibility to many viral diseases. However, a variety of challenges have made the implementation of traditional human Genome-wide Association Studies (GWAS) approaches to study these infectious outcomes challenging. In contrast, mouse models of infectious diseases provide an experimental control and precision, which facilitates analyses and mechanistic studies of the role of genetic variation on infection. Here we use a genetic mapping cross between two distinct Collaborative Cross mouse strains with respect to severe acute respiratory syndrome coronavirus (SARS-CoV) disease outcomes. We find several loci control differential disease outcome for a variety of traits in the context of SARS-CoV infection. Importantly, we identify a locus on mouse chromosome 9 that shows conserved synteny with a human GWAS locus for SARS-CoV-2 severe disease. We follow-up and confirm a role for this locus, and identify two candidate genes, CCR9 and CXCR6, that both play a key role in regulating the severity of SARS-CoV, SARS-CoV-2, and a distantly related bat sarbecovirus disease outcomes. As such we provide a template for using experimental mouse crosses to identify and characterize multitrait loci that regulate pathogenic infectious outcomes across species. IMPORTANCE Host genetic variation is an important determinant that predicts disease outcomes following infection. In the setting of highly pathogenic coronavirus infections genetic determinants underlying host susceptibility and mortality remain unclear. To elucidate the role of host genetic variation on sarbecovirus pathogenesis and disease outcomes, we utilized the Collaborative Cross (CC) mouse genetic reference population as a model to identify susceptibility alleles to SARS-CoV and SARS-CoV-2 infections. Our findings reveal that a multitrait loci found in chromosome 9 is an important regulator of sarbecovirus pathogenesis in mice. Within this locus, we identified and validated CCR9 and CXCR6 as important regulators of host disease outcomes. Specifically, both CCR9 and CXCR6 are protective against severe SARS-CoV, SARS-CoV-2, and SARS-related HKU3 virus disease in mice. This chromosome 9 multitrait locus may be important to help identify genes that regulate coronavirus disease outcomes in humans.

Animals↗
PubMed2000

[Prediction and evaluation of heterosis of beef cattle and their application].

The genetic structure and genetic variation of eight beef cattle cross parents populations were analyzed by six microsatellite loci, and heterosis of beef cattle was predicted. On the basis of microsatellite analysis, the effect of 18 cross combinations was estimated by the method of individual animal model BLUP. A new method of molecular quantitative genetics that select best of all cross combination was submitted. The results showed that the combinations with Hereford Limousine and Charolais as paternal parent are better than others in Fengning and Longhua regions; the combinations with Limousine Angus and Hereford as paternal parent are better than others in Zanhuang regions; the combinations with Hereford Limousine and Piemontese as paternal parent are better than others in Funing regions. Effect of three breeds cross is better than two breeds.

Animals↗
PubMed2005

[RAPD analysis on genetic diversity of the preconcentrated core germplasms of Camellia Sinensis in China].

The study was to evaluate the genetic diversity of 69 tea cultivars of the preconcentrated core germplasms of Camellia Sinensis in China by the random amplified polymorphic DNA (RAPD). Among 50 arbitrary primers, 32 primers could generate enough amplified bands for all the strains in this study. Among a total of 348 bands observed, 328 (94.3%)bands were polymorphic in the 69 cultivars tested except additional 20 cultivars. Genetic distances between the cultivars varied from 0.223 to 0.723. The study indicated that the pre-concentrated core germplasms of Camellia Sinensis in China could well represent the whole collection in respect of genetic structure and genetic diversity and genetic distance. At the same time, it was the best option to establish core collection of Camellia Sinensis in China by combining morphological markers with DNA molecular markers.

Base Sequence↗
PubMed2006

Isolation by resistance.

Despite growing interest in the effects of landscape heterogeneity on genetic structuring, few tools are available to incorporate data on landscape composition into population genetic studies. Analyses of isolation by distance have typically either assumed spatial homogeneity for convenience or applied theoretically unjustified distance metrics to compensate for heterogeneity. Here I propose the isolation-by-resistance (IBR) model as an alternative for predicting equilibrium genetic structuring in complex landscapes. The model predicts a positive relationship between genetic differentiation and the resistance distance, a distance metric that exploits precise relationships between random walk times and effective resistances in electronic networks. As a predictor of genetic differentiation, the resistance distance is both more theoretically justified and more robust to spatial heterogeneity than Euclidean or least cost path-based distance measures. Moreover, the metric can be applied with a wide range of data inputs, including coarse-scale range maps, simple maps of habitat and nonhabitat within a species' range, or complex spatial datasets with habitats and barriers of differing qualities. The IBR model thus provides a flexible and efficient tool to account for habitat heterogeneity in studies of isolation by distance, improve understanding of how landscape characteristics affect genetic structuring, and predict genetic and evolutionary consequences of landscape change.

Biological Evolution↗
PubMed2005

Comparative host-parasite population structures: disentangling prospecting and dispersal in the black-legged kittiwake Rissa tridactyla.

Although much insight is to be gained through the comparison of the population genetic structures of parasites and hosts, there are, at present, few studies that take advantage of the information on vertebrate life histories available through the consideration of their parasites. Here, we examined the genetic structure of a colonial seabird, the black-legged kittiwake (Rissa tridactyla) using seven polymorphic microsatellite markers to make inferences about population functioning and intercolony dispersal. We sampled kittiwakes from 22 colonies across the species' range and, at the same time, collected individuals of one of its common ectoparasites, the tick Ixodes uriae. Parasites were genotyped at eight microsatellite markers and the population genetic structure of host and parasite were compared. Kittiwake populations are only genetically structured at large spatial scales and show weak patterns of isolation by distance. This may be due to long-distance dispersal events that erase local patterns of population subdivision. However, important additional information is gained by comparing results with those of the parasite. In particular, tick populations are strongly structured at regional scales and show a stepping-stone pattern of gene flow. Due to the parasite's life history, its population structure is directly linked to the frequency and spatial extent of within-breeding season movements of kittiwakes. The comparison of host and parasite gene flow therefore helps us to disentangle the intercolony movements of birds from that of true dispersal events (movement followed by reproduction). In addition, such data can provide essential elements for predicting the outcome of local co-evolutionary interactions.

Animals↗