Nesting biology and DNA barcode analysis of Ceratina dupla and C. mikmaqi, and comparisons with C. calcarata (Hymenoptera: Apidae: Xylocopinae)

2011 ◽  
Vol 143 (3) ◽  
pp. 254-262 ◽  
Author(s):  
J.L. Vickruck ◽  
S.M. Rehan ◽  
C.S. Sheffield ◽  
M.H. Richards
Keyword(s):  
Dna Barcode ◽  
Sequence Divergence ◽  
Nesting Biology ◽  
Southern Ontario ◽  
Average Sequence Divergence ◽  
Nesting Behaviour ◽  
Average Sequence

AbstractUsing DNA barcode analysis, nest collections, and pan-trapping we compared molecular differences, nesting behaviour, and phenology of three of the four species of Ceratina Latreille present in the Niagara Region of southern Ontario, Canada: C. dupla Say, C. calcarata Robertson, and C. mikmaqi Rehan and Sheffield. Ceratina dupla and C. mikmaqi were separated by five fixed nucleotide differences and an average sequence divergence of 1.86%. In our population, C. mikmaqi and C. calcarata were common and C. dupla was rare. Ceratina dupla nested earlier than C. mikmaqi and C. calcarata, and sometimes produced a second brood in late July – early August. Each species constructed linear nests in the pith of dead twigs, C. mikmaqi and C. dupla usually in Fuller's teasel (Dipsacus fullonum L.; Dipsacaceae) and C. calcarata usually in raspberry (Rubus L.; Rosaceae). Genetically distinct, each species occupies a slightly different niche in the Niagara bee assemblage.

scholarly journals Homology of Escherichia coli R773 arsA, arsB, and arsC Genes in Arsenic-Resistant Bacteria Isolated from Raw Sewage and Arsenic-Enriched Creek Waters

2002 ◽  
Vol 68 (1) ◽  
pp. 280-288 ◽  
Author(s):  
Chad W. Saltikov ◽  
Betty H. Olson
Keyword(s):  
Escherichia Coli ◽  
Sequence Divergence ◽  
Enteric Bacteria ◽  
Resistant Bacteria ◽  
Colony Hybridization ◽  
E Coli ◽  
Average Sequence Divergence ◽  
Significant Divergence ◽  
Average Sequence ◽  
Arsenic Resistant Bacteria

ABSTRACT The occurrence and diversity of the Escherichia coli R773 ars operon were investigated among arsenic-resistant enteric and nonenteric bacteria isolated from raw sewage and arsenic-enriched creek waters. Selected isolates from each creek location were screened for ars genes by colony hybridization and PCR. The occurrence of arsA, arsB, and arsC determined by low-stringency colony hybridization (31 to 53% estimated mismatch) was 81, 87, and 86%, respectively, for 84 bacteria isolated on arsenate- and arsenite-amended media from three locations. At moderate stringency (21 to 36% estimated mismatch), the occurrence decreased to 42, 56, and 63% for arsA, arsB, and arsC, respectively. PCR results showed that the ars operon is conserved in some enteric bacteria isolated from creek waters and raw sewage. The occurrence of the arsBC genotype was about 50% in raw sewage enteric bacteria, while arsA was detected in only 9.4% of the isolates (n = 32). The arsABC and arsBC genotypes occurred more frequently in enteric bacteria isolated from creek samples: 71.4 and 85.7% (n = 7), respectively. Average sequence divergence within arsB for six creek enteric bacteria was 20% compared to that of the E. coli R773 ars operon. Only 1 of 11 pseudomonads screened by PCR was positive for arsB. The results from this study suggest that significant divergence has occurred in the ars operon among As-resistant E. coli strains and in Pseudomonas spp.

scholarly journals Hepatitis B virus genotype G epidemiology and co-infection with genotype A in Canada

2008 ◽  
Vol 89 (12) ◽  
pp. 3009-3015 ◽  
Author(s):  
Carla Osiowy ◽  
Diane Gordon ◽  
Jamie Borlang ◽  
Elizabeth Giles ◽  
Jean-Pierre Villeneuve
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Sequence Divergence ◽  
Virus Genotype ◽  
Hbv Genotype ◽  
B Virus ◽  
Average Sequence Divergence ◽  
Unusual Variant ◽  
Average Sequence ◽  
Genotype A

Hepatitis B virus (HBV) genotype G (HBV/G) is an unusual variant, and little is known about its epidemiology and natural history, particularly the requirement for a co-infecting HBV genotype and their relationship during infection. This study investigated the quasispecies nature of co-infecting genotypes in 39 samples collected over a 6 year period from 13 HBV/G-infected patients. HBV/G infections were found to occur predominantly in males (92 %) and were primarily associated with male homosexual sex (67 %). All patients were infected with HBV/G and HBV/A, or a recombinant HBV/A/G strain. Co-infecting genotypic prevalence was often observed to fluctuate over time, with periods of HBV/G monoinfection in some patients. The average sequence divergence among Canadian HBV/G strains was 1.57±0.62 %. Thus, all HBV/G infections in Canada occur in the context of co-infection or recombination with HBV/A, and strains display increased sequence divergence compared with all known HBV/G sequences described to date.

Restriction Analysis of Mitochondrial DNA from the Yellow-footed Rock-wallaby, Petrogale xanthopus: Implications for Management

1997 ◽  
Vol 24 (3) ◽  
pp. 289 ◽  
Author(s):  
M. D. B. Eldridge
Keyword(s):  
Mitochondrial Dna ◽  
New South ◽  
Restriction Analysis ◽  
Sequence Divergence ◽  
South Australia ◽  
Unique Haplotype ◽  
South Wales ◽  
In Captivity ◽  
Average Sequence Divergence ◽  
Average Sequence

The extent of mitochondrial DNA divergence between populations of the vulnerable yellow-footed rock- wallaby, Petrogale xanthopus, was assessed by restriction analysis. Of the 15 restriction endonucleases, five were informative, with a single unique haplotype identified in P. x. celeris from Queensland (Qld) (n = 8) and a further two unique haplotypes in three sampled populations of P. x. xanthopus from New South Wales (NSW) (n = 1) and South Australia (SA) (n = 9). The two subspecies of P. xanthopus were found to be genetically distinct (average sequence divergence = 0·72%). As this divergence is greater than that found between some Petrogale species, it is recommended that populations of P. x. xanthopus and P. x. celeris be managed independently both in captivity and the wild. The NSW population of P. x. xanthopus appears genetically similar to those in SA, although these data are limited.

scholarly journals Phenology and Synchrony of Scymnus coniferarum (Coleoptera: Coccinellidae) with Multiple Adelgid Species in the Puget Sound, WA, USA

Forests ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 558
Author(s):  
Molly Darr ◽  
Rachel Brooks ◽  
Nathan Havill ◽  
E. Hoebeke ◽  
Scott Salom
Keyword(s):  
Biological Control ◽  
Puget Sound ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Adelges Tsugae ◽  
Tsuga Heterophylla ◽  
Seasonal Abundance ◽  
Invasive Pest ◽  
Pinus Monticola ◽  
Conifer Species

The hemlock woolly adelgid (HWA), Adelges tsugae, is an invasive pest of Tsuga spp. in eastern North America. Scymnus coniferarum is a predaceous beetle that was collected from HWA in the western United States. Limited knowledge of this insect in its native habitat led to studies to evaluate its potential for biological control of HWA. Seasonal abundance was sampled at six sites in Tacoma, WA, twice monthly, for one year on different host trees of potential adelgid prey. Tree species included Pseudotsuga menziesii, Pinus contorta, Pinus monticola, and Tsuga heterophylla. Scymnus coniferarum adults were found on all conifer species, except P. menziesii. Each conifer species supported a different adelgid species, suggesting S. coniferarum feeds on multiple adelgid species. More S. coniferarum were found on pine than hemlock. DNA barcoding of S. coniferarum found two distinct clusters that differed by 6% divergence. Beetles in each cluster were co-habiting the same conifer species, and they could not be distinguished morphologically. Further taxonomic studies are needed to understand the significance of DNA barcode sequence divergence. Because S. coniferarum was more frequently associated with pine adelgids than HWA, and because of remaining taxonomic uncertainty, S. coniferarum may not be suitable for HWA biological control.

scholarly journals Comparative Plastid Genomics of Four Pilea (Urticaceae) Species: Insight into Interspecific Plastid Genome Diversity in Pilea

2020 ◽  
Author(s):  
Jingling Li ◽  
Jianmin Tang ◽  
Siyuan Zeng ◽  
Fang Han ◽  
Jing Yuan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Plastid Genome ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Hypervariable Regions ◽  
Plastid Genomes ◽  
Insight Into

Abstract Background: Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis.Results: The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.Conclusion: Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

scholarly journals Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

2017 ◽  
Author(s):  
Milan Malinsky ◽  
Hannes Svardal ◽  
Alexandra M. Tyers ◽  
Eric A. Miska ◽  
Martin J. Genner ◽  
...  
Keyword(s):  
Gene Flow ◽  
Fish Species ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Sequence Divergence ◽  
Single Species ◽  
Lake Malawi ◽  
Genomic Diversity ◽  
Average Sequence Divergence ◽  
Deep Water Species

AbstractThe hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalistAstatotilapia-likeancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.

scholarly journals Barcoding ciliates: a comprehensive study of 75 isolates of the genus Tetrahymena

2007 ◽  
Vol 57 (10) ◽  
pp. 2412-2423 ◽  
Author(s):  
Chitchai Chantangsi ◽  
Denis H. Lynn ◽  
Maria T. Brandl ◽  
Jeffrey C. Cole ◽  
Neil Hetrick ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Sequence Divergence ◽  
Tetrahymena Pyriformis ◽  
Order Of Magnitude ◽  
Nj Tree ◽  
The Mean ◽  
Taxonomic Marker ◽  
The One ◽  
Close Relatives ◽  
Comprehensive Study

The mitochondrial cytochrome-c oxidase subunit 1 (cox1) gene has been proposed as a DNA barcode to identify animal species. To test the applicability of the cox1 gene in identifying ciliates, 75 isolates of the genus Tetrahymena and three non-Tetrahymena ciliates that are close relatives of Tetrahymena, Colpidium campylum, Colpidium colpoda and Glaucoma chattoni, were selected. All tetrahymenines of unproblematic species could be identified to the species level using 689 bp of the cox1 sequence, with about 11 % interspecific sequence divergence. Intraspecific isolates of Tetrahymena borealis, Tetrahymena lwoffi, Tetrahymena patula and Tetrahymena thermophila could be identified by their cox1 sequences, showing <0.65 % intraspecific sequence divergence. In addition, isolates of these species were clustered together on a cox1 neighbour-joining (NJ) tree. However, strains identified as Tetrahymena pyriformis and Tetrahymena tropicalis showed high intraspecific sequence divergence values of 5.01 and 9.07 %, respectively, and did not cluster together on a cox1 NJ tree. This may indicate the presence of cryptic species. The mean interspecific sequence divergence of Tetrahymena was about 11 times greater than the mean intraspecific sequence divergence, and this increased to 58 times when all isolates of species with high intraspecific sequence divergence were excluded. This result is similar to DNA barcoding studies on animals, indicating that congeneric sequence divergences are an order of magnitude greater than conspecific sequence divergences. Our analysis also demonstrated low sequence divergences of <1.0 % between some isolates of T. pyriformis and Tetrahymena setosa on the one hand and some isolates of Tetrahymena furgasoni and T. lwoffi on the other, suggesting that the latter species in each pair is a junior synonym of the former. Overall, our study demonstrates the feasibility of using the mitochondrial cox1 gene as a taxonomic marker for ‘barcoding’ and identifying Tetrahymena species and some other ciliated protists.

Nesting biology and subsociality in Ceratina calcarata (Hymenoptera: Apidae)

2010 ◽  
Vol 142 (1) ◽  
pp. 65-74 ◽  
Author(s):  
Sandra M. Rehan ◽  
Miriam H. Richards
Keyword(s):  
Life History ◽  
Adult Development ◽  
Social Life ◽  
North American Species ◽  
Nesting Biology ◽  
Southern Ontario ◽  
Active Season ◽  
Carpenter Bees ◽  
Nest Founding ◽  
Ceratina Calcarata

AbstractTo evaluate sociality in small carpenter bees (Ceratina Latreille), we studied the life history and nesting biology of a common eastern North American species, Ceratina (Zadontomerus) calcarata Robertson. Pan-trap and nest collections throughout the active season (May to September 2006) were used to assess C. calcarata’s seasonal phenology and nesting biology in southern Ontario. Adults overwintered in their natal nests. Males emerged in early May and occupied preexisting hollows in twigs and stems. Females emerged from hibernacula 2 weeks later, founding new nests. Nest founding and provisioning occurred throughout the spring; females remained with developing brood through the summer. Complete nests contained, on average, 6.9 offspring, with egg-to-adult development averaging 46 days. Ceratina calcarata is subsocial rather than solitary: mothers are long-lived and nest-loyal, and care for offspring from egg to adulthood. Subsociality is found in all behaviourally classified small carpenter bees, while some species cross the boundary into social life, making Ceratina an important genus for the study of the transition between solitary and social life.

Insights into size, seasonality and biology of a nesting population of the Olive Ridley turtle in northern Australia

2007 ◽  
Vol 34 (3) ◽  
pp. 200 ◽  
Author(s):  
Scott D. Whiting ◽  
John L. Long ◽  
Kate M. Hadden ◽  
Anderson D. K. Lauder ◽  
Andrea U. Koch
Keyword(s):  
Canis Lupus ◽  
Olive Ridley ◽  
Nesting Biology ◽  
South East Asian Region ◽  
Lepidochelys Olivacea ◽  
Marine Turtles ◽  
Nesting Behaviour ◽  
Crocodylus Porosus ◽  
Olive Ridley Turtle ◽  
Nesting Season

The Olive Ridley turtle (Lepidochelys olivacea), classed as endangered in Australia, is one of Australia’s least studied marine turtles and is little known in the south-east Asian region. This is the first detailed study of the nesting biology and ecology of L. olivacea in Australia or south-east Asia, which adds to the regional knowledge of the species and will aid management locally. Daytime surveys of nesting tracks at 14-day intervals in 2004 and irregular surveys in 2005 indicated that the nesting season extended from February to November with peak nesting in April and May. Daily track counts over a 14-day period in April 2004 during peak nesting showed that nesting abundance varied between nights and along the beach. Nightly numbers ranged from 2 to 59 turtles per night over the 10-km beach while, spatially, nesting densities (0.1–6.9 tracks km–1 night–1) varied between sectors. Nesting in this population was solitary, as opposed to the mass nesting behaviour of L. olivacea observed elsewhere in its range, such as in India, Mexico and Costa Rica. The size of nesting L. olivacea was normally distributed with a mean curved carapace length of 69.6 ± 2.3 (s.d.) cm (range = 65.0–75.2, n = 85). During the peak of the nesting season dingoes (Canis lupus dingo) were responsible for the highest egg mortality (over 14%), followed by varanids (Varanus spp., 4.5%) and humans (1.7%). Cyclone Ingrid caused significant egg loss in 2004. Saltwater crocodiles (Crocodylus porosus) were a significant predator of adult nesting turtles.

scholarly journals Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingling Li ◽  
Jianmin Tang ◽  
Siyuan Zeng ◽  
Fang Han ◽  
Jing Yuan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Plastid Genome ◽  
Dna Barcode ◽  
Sequence Divergence ◽  
Rrna Genes ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Hypervariable Regions ◽  
Plastid Genomes ◽  
Insight Into

Abstract Background Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca ‘Greizy’, Pilea peperomioides and Pilea serpyllacea ‘Globosa’) and performed comprehensive comparative analysis. Results The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. Conclusion Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.

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