scholarly journals A Biological Analysis on the Invasiveness of the Corbicula Fluminea

2021 ◽  
Vol 9 (3) ◽  
Author(s):  
Sreyas Yeddula ◽  
Akshay Jakkidi Reddy ◽  
Eric Liu ◽  
Himanshu Wagh
Keyword(s):  
Native American ◽  
Dna Analysis ◽  
Central Valley ◽  
Corbicula Fluminea ◽  
Relative Advantage ◽  
Filter Feeder ◽  
Genetic Traits ◽  
American River ◽  
Feeding Methods ◽  
Food Particles

Corbicula fluminea is an invasive species that has been observed to outcompete the native clams at the American River located near Sacramento in the Central Valley in California. We hypothesized that C. Fluminea has advantages exhibited physically including utilization of filter-feeding methods and relative spacing of its cirri as compared to the native American River clams. To investigate what makes the species so successful, we tested C. Fluminea versus the native clams in algal and E.coli environments to predict the relative advantage of a filter feeder. In addition, we used computer programs to digitally analyze the spacing between the actual cirri, which help bivalves capture food particles, of the two species. The findings pointed towards C. Fluminea’s inherent advantage in both physical and genetic traits over the native clams species which allowed it to flourish and successfully invade the American River ecosystem. However, the species’ genetic findings are found through DNA analysis.

scholarly journals Ancient DNA Analysis of Archaeological Specimens Extends Chinook Salmon’s Known Historic Range to San Francisco Bay and Its Southernmost Watershed

2020 ◽  
Author(s):  
Richard B. Lanman ◽  
Linda Hylkema ◽  
Cristie M. Boone ◽  
Brian Alleé ◽  
Roger O. Castillo ◽  
...  
Keyword(s):  
Native American ◽  
San Francisco ◽  
Ancient Dna ◽  
Chinook Salmon ◽  
Habitat Restoration ◽  
Dna Analysis ◽  
Oncorhynchus Tshawytscha ◽  
San Francisco Bay ◽  
Bay Area ◽  
Guadalupe River

Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon ( Oncorhynchus tshawytscha ) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropomorphic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Using ichthyofaunal analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara circa 1781-1834 CE, 86 salmonid vertebrae were identified. Ancient DNA sequencing identified three of these as from Chinook salmon and the remainder from steelhead trout. These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their historic range to include San Francisco Bay’s southernmost watershed.

scholarly journals Resequencing DCDC5 in the Flanking Region of an LD-SNP Derived from a Kidney-Yang Deficiency Syndrome Family

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Li Ping Zhou ◽  
Wei Wei Liu ◽  
Tian E. Zhang ◽  
Wei Hong Li ◽  
Ling Ling Tan ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Substitution Effect ◽  
Deficiency Syndrome ◽  
Trna Synthetase ◽  
Genomic Variation ◽  
Single Nucleotide ◽  
Genetic Traits ◽  
Kidney Yang Deficiency ◽  
Flanking Region ◽  
Nonsynonymous Variation

Objective. To explore the genetic traits of Kidney-yang deficiency syndrome (KDS).Design. Twelve KDS subjects and three spouses from a typical KDS family were recruited. Their genomic DNA samples were genotyped by Affymetrix 100K single-nucleotide polymorphism (SNP) arrays. The linkage disequilibrium (LD) SNPs were generated using GeneChip DNA analysis software (GDAS, Affymetrix). Genes located within 100 bp of the flanks of LD SNPs were mined via GeneView. 29 exons of the doublecortin domain containing 5 (DCDC5), a representative gene within the flank of an LD SNP, were resequenced.Results. Five LD SNPs display midrange linkage with KDS. Two genes with established functions, DCDC5 and Leucyl-tRNA synthetase, were mined in the flanks of LD SNPs. Resequencing of DCDC5 revealed a nonsynonymous variation, in which 3764T/A was replaced by C/G. Accordingly, the Ser1172was substituted by Pro1172. The S1172P substitution effect was evaluated as “possibly damaging” by PolyPhen.Conclusion. We have identified a genomic variation of DCDC5 based on the LD SNPs derived from a KDS family. DCDC5 and other genes surrounding these SNPs display some relationships with key symptoms of KDS.

scholarly journals Randomly Amplified Polymorphic DNA Analysis in the Genus Hosta

HortScience ◽  
2005 ◽  
Vol 40 (5) ◽  
pp. 1243-1245 ◽  
Author(s):  
Roger J. Sauve ◽  
Suping Zhou ◽  
Yingchun Yu ◽  
Wolfram George Schmid
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Genetic Traits ◽  
Phylogenetic Clustering ◽  
Single Primer ◽  
Cluster 2

A randomly amplified polymorphic DNA (RAPD) technique was used to identify and determine the phylogenetic relationships of 37 hosta accessions representing the major subgenera, sections and groups in the genus Hosta. Results of this study show that RAPD markers were able to differentiate not only the main groups, whose plants shared many genetic traits, but also cultivars within a species. Some accessions were identified by a single primer while others had high intercross linkage and required many markers for their separation. The phylogenetic clustering showed that H. plantaginea, the only night-blooming species, and H. ventricosa, the only known natural tetraploid, are unique and should be classified separately. The four species in the subgenus Bryocles, section Lamellatae H. venusta, H. minor, H. capitata, and H. nakaiana have very low genetic similarity since they do not share many amplified fragments. The other accessions were classified into four main clusters; cluster 1: H. venusta, H. tardiva, H. pycnophylla, H. tsushimensis `Ogon', H. montana, H. tibae, H. montana f. macrophylla, H. kikutii `Kikutii', H. longissima `Longifolia', H. rectifolia `Rectifolia', H. takahashii and H.`Undulata'; cluster 2: H. laevigata, H. sieboldiana, H. pycnophylla × H. longipes f. latifolia, H. longipes `Urajiro' and H. ibukiensis; cluster 3: H. capitata, H. kikutii `Polyneuron', H. nigrescens, H. kikutii `Yakusimensis', H. pachyscapa, H. kikutii `Caput-Avis', H. longipes f. latifolia, H. hypoleuca, H. okamotoi, H. densa and H. takiensis; and cluster 4: H. aequinoctiiantha, H. rupifraga, H. `Amanuma', H. minor and H. kikutii `Densa'.

scholarly journals Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 153-162 ◽  
Author(s):  
A Torroni ◽  
T G Schurr ◽  
C C Yang ◽  
E J Szathmary ◽  
R C Williams ◽  
...  
Keyword(s):  
Native American ◽  
American Indians ◽  
Sequence Variation ◽  
Dna Analysis ◽  
Restriction Analysis ◽  
Divergence Time ◽  
Divergence Times ◽  
South American ◽  
Genetic Stock ◽  
Mitochondrial Dnas

Abstract Mitochondrial DNAs (mtDNAs) from 167 American Indians including 87 Amerind-speakers (Amerinds) and 80 Nadene-speakers (Nadene) were surveyed for sequence variation by detailed restriction analysis. All Native American mtDNAs clustered into one of four distinct lineages, defined by the restriction site variants: HincII site loss at np 13,259, AluI site loss at np 5,176, 9-base pair (9-bp) COII-tRNA(Lys) intergenic deletion and HaeIII site gain at np 663. The HincII np 13,259 and AluI np 5,176 lineages were observed exclusively in Amerinds and were shared by all such tribal groups analyzed, thus demonstrating that North, Central and South American Amerinds originated from a common ancestral genetic stock. The 9-bp deletion and HaeIII np 663 lineages were found in both the Amerinds and Nadene but the Nadene HaeIII np 663 lineage had a unique sublineage defined by an RsaI site loss at np 16,329. The amount of sequence variation accumulated in the Amerind HincII np 13,259 and AluI np 5,176 lineages and that in the Amerind portion of the HaeIII np 663 lineage all gave divergence times in the order of 20,000 years before present. The divergence time for the Nadene portion of the HaeIII np 663 lineage was about 6,000-10,000 years. Hence, the ancestral Nadene migrated from Asia independently and considerably more recently than the progenitors of the Amerinds. The divergence times of both the Amerind and Nadene branches of the COII-tRNA(Lys) deletion lineage were intermediate between the Amerind and Nadene specific lineages, raising the possibility of a third source of mtDNA in American Indians.

Mitochondrial DNA Analysis Reveals Substantial Native American Ancestry in Puerto Rico

Human Biology ◽  
2001 ◽  
Vol 73 (4) ◽  
pp. 491-511 ◽  
Author(s):  
J. C. Martinez-Cruzado ◽  
G Toro-Labrador ◽  
V Ho-Fung ◽  
M Estevez-Montero ◽  
A Lobaina-Manzanet ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Puerto Rico ◽  
Native American ◽  
Dna Analysis ◽  
Native American Ancestry ◽  
Mitochondrial Dna Analysis

scholarly journals Anadromy Redux? Genetic Analysis to Inform Development of an Indigenous American River Steelhead Broodstock

2019 ◽  
Vol 10 (1) ◽  
pp. 137-147
Author(s):  
Alicia Abadía-Cardoso ◽  
Annie Brodsky ◽  
Bradley Cavallo ◽  
Martha Arciniega ◽  
John Carlos Garza ◽  
...  
Keyword(s):  
Central Valley ◽  
Genomic Variation ◽  
Spawning Habitat ◽  
Distinct Population ◽  
Negative Effects ◽  
Fish Hatchery ◽  
Distinct Population Segment ◽  
American River ◽  
Hatchery Program ◽  
Population Segment

Abstract The construction of dams and water diversions has severely limited access to spawning habitat for anadromous fishes. To mitigate for these impacts, hatchery programs rear and release millions of juvenile salmonids, including steelhead, the anadromous ecotype of the species Oncorhynchus mykiss. These programs sometimes use nonindigenous broodstock sources that may have negative effects on wild populations. In California, however, only one anadromous fish hatchery program currently uses nonnative broodstock: the steelhead program at Nimbus Fish Hatchery on the American River, a tributary of the Sacramento River in the California Central Valley. The goal of this study was to determine if potentially appropriate sources to replace the broodstock for the Nimbus Hatchery steelhead program exist in the Upper American River, above Nimbus and Folsom dams. We show that all Upper American River O. mykiss sampled share ancestry with other populations in the Central Valley steelhead distinct population segment, with limited introgression from out-of-basin sources in some areas. Furthermore, some Upper American River populations retain adaptive genomic variation associated with a migratory life history, supporting the hypothesis that these populations display adfluvial migratory behavior. Together, these results provide insights into the evolution of trout populations above barrier dams. We conclude that some Upper American River O. mykiss populations represent genetically appropriate sources from which fisheries managers could potentially develop a new broodstock for the Nimbus Hatchery steelhead program to reestablish a native anadromous population in the Lower American River and contribute to recovery of the threatened Central Valley steelhead distinct population segment.

scholarly journals HUMAN BEING AS THE BEARER OF IDENTIFYING BIOLOGICAL INFORMATION

2021 ◽  
Author(s):  
L. Кotliarenko ◽  
А. Коfanov ◽  
O. Коfаnоvа ◽  
V. Zherebak
Keyword(s):  
Genetic Analysis ◽  
Dna Analysis ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Molecular Genetic Analysis ◽  
Genetic Identification ◽  
Criminal Proceedings ◽  
Genetic Traits ◽  
Criminal Offenses ◽  
Genetic Examination

In forensic practice, biological traces of a person are very often used as material evidence - blood, hair, saliva, semen, urine, sweat, as well as parts of organs and tissues. Establishing the origin of these traces from a specific person is very important for the investigation of criminal offenses. The current level of development of molecular genetic research indicates the need to use DNA analysis in the detection and investigation of criminal offenses against a person. Today, molecular genetic identification reveal reliable prospects for solving identification problems in the criminal proceedings and developing the evidence base, and also has a number of advantages over traditional serological methods for studying human biological traces. It should be noted that along with the traditional method of nuclear DNA research, mitochondrial DNA research is also being carried out, which allows solving the problem of molecular genetic examination to establish biological affinity. The value of this method lies in its effectiveness in the study of a small amount of degraded DNA, secretions and heavily damaged objects, the study of which is impossible by traditional methods. When performing a forensic molecular genetic examination for the full identification of the detected traces when examining the places of committed criminal offenses, comparative samples are important, as well as the selection of appropriate biological samples to establish paternity and family ties. Molecular genetic analysis of DNA is only one of the stages of identification, and in order to arrive at the final result, a statistical analysis of the data obtained is necessary, which is especially important when the genotypes of the criminal and the suspect in mixed tracks coincide. For a probable-statistical assessment of the results of the identification significance of the set of established genetic traits, the frequencies of the distribution of the studied alleles in the population are required. Today, the DNA analysis method has become one of the most demanded directions in the development of forensic examinations, and its results are quite reliable evidence of the involvement of a specific person in a crime. Due to its unique capabilities, molecular genetic analysis of DNA is a powerful tool in the investigation of criminal proceedings.

Ecology and Biogeography of Living Classes

1980 ◽  
Vol 3 ◽  
pp. 1-14
Author(s):  
David L. Meyer
Keyword(s):  
Sea Cucumber ◽  
Water Mass ◽  
Food Preferences ◽  
Great Depth ◽  
Marine Organisms ◽  
Sea Floor ◽  
Anomalous Form ◽  
Feeding Methods ◽  
Food Particles ◽  
Living Group

Trophic classification. Appreciation of the ecologic functions of echinoderms is derived from an understanding of the diverse feeding methods and food preferences found within the group. Echinoderms are dominantly benthonic marine organisms but exploit a wide variety of food resources on the bottom, within the sediment, and from the water masses near the bottom (Table 1). The only echinoderms that are not strictly benthonic are some of the elasipodid holothurians, which have been captured at the surface and swimming above the bottom at great depth (Barnes et al., 1976). By rhythmic undulations of a fan of oral tentacles these bizarre holothurians capture suspended food particles from the water mass near the sea floor. Their anomalous form and habits, so far removed from the typical sea cucumber, serve to emphasize that holothurians and all other echinoderms cannot be readily characterized by a single trophic classification for each group. Each major living group of echinoderms has diversified in feeding methods and/or food preferences.

scholarly journals Mitochondrial DNA analysis suggests a Chibchan migration into Colombia

2015 ◽  
Vol 20 (2) ◽  
pp. 261 ◽  
Author(s):  
Maria Claudia Noguera-Santamaría ◽  
Carl Edlund Anderson ◽  
Daniel Uricoechea ◽  
Clemencia Durán ◽  
Ignacio Briceño-Balcázar ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Native American ◽  
Dna Analysis ◽  
Human Genetics ◽  
Human Populations ◽  
South American ◽  
Indigenous Groups ◽  
Genetic Structures

The characterization of mitochondrial DNA (mtDNA) allows the establishment of genetic structures and phylogenetic relationships in human populations, tracing lineages far back in time. We analysed samples of mtDNA from twenty (20) Native American populations (700 individuals) dispersed throughout Colombian territory. Samples were collected during 1989-1993 in the context of the program Expedición Humana (“Human Expedition”) and stored in the Biological Repository of the Institute of Human Genetics (IGH) at the Pontificia Universidad Javeriana (Bogotá, Colombia). Haplogroups were determined by analysis of RFLPs. Most frequent was haplogroup A, with 338 individuals (48.3%). Haplogroup A is also one of the most frequent haplogroups in Mesoamerica, and we interpret our finding as supporting models that propose Chibchan-speaking groups migrated to northern Colombia from Mesoamerica in prehistoric times. Haplogroup C was found in 199 individuals (28.4%), while less frequent were B and D, with 113 and 41 (16% and 6%) individuals, respectively. The haplogroups of nine (9) individuals (1.3%) could not be determined due to the low quality of the samples of DNA. Although all the sampled populations had genetic structures that fit broadly into the patterns that might be expected for contemporary Central and South American indigenous groups, it was found that haplogroups A and B were more frequent in northern Colombia, while haplogroups C and D were more frequent in southern and south-western Colombia.

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