Origins of an Anasazi Scarlet Macaw Feather Artifact

1998 ◽  
Vol 63 (1) ◽  
pp. 131-142 ◽  
Author(s):  
Nancy Borson ◽  
Frances Berdan ◽  
Edward Stark ◽  
Jack States ◽  
Peter J. Wettstein
Keyword(s):  
Molecular Biology ◽  
Ancient Dna ◽  
Phylogenetic Trees ◽  
American Southwest ◽  
The Other ◽  
Neighbor Joining ◽  
Nucleotide Substitutions ◽  
Construction Technique ◽  
Scarlet Macaw ◽  
Prior Hypothesis

An artifact ascribed to the Anasazi culture (dated here to 920 ± 35 B.P.) is unique in its integrity, construction technique, style, and materials, including multiple yucca ropes with attached adult scarlet macaw feathers joined to a Sciurus aberti (tassel-eared squirrel) pelt and hide straps. We applied methods from anthropology and molecular biology to ascertain the origins of materials and manufacturing technique. The cytochrome b gene from the ancient DNA of the pelt was sequenced in its entirety. This gene was unique as defined by new nucleotide substitutions that distinguished it from the other S. aberti alleles. Phylogenetic trees constructed by both neighbor-joining and maximum parsimony methods are consistent with this unique allele being most closely related to genes from two extant American Southwest S. aberti subspecies and more distantly related to Mexican S. aberti genes. Our observations support the conclusion that the entire artifact was constructed in the American Southwest using native materials, including the squirrel pelt and scarlet macaw feathers. This contradicts a prior hypothesis that the feather rope component was assembled before being traded north from Mexico.

scholarly journals Variation of the Ribosomal Operon 16S-23S Gene Spacer Region in Representatives of Salmonella enterica Subspecies

1998 ◽  
Vol 180 (8) ◽  
pp. 2144-2151 ◽  
Author(s):  
Sara Pérez Luz ◽  
Francisco Rodríguez-Valera ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Salmonella Enterica ◽  
Phylogenetic Trees ◽  
Housekeeping Genes ◽  
The Other ◽  
Nucleotide Substitutions ◽  
E Coli ◽  
The Family ◽  
Ribosomal Operon ◽  
Ribosomal Operons ◽  
K 12

ABSTRACT The 16S-23S spacer regions of two ribosomal operons (rrnA and rrnE) have been sequenced in seven representatives of the Salmonella entericasubspecies. Isolated nucleotide substitutions were found at the same sites as in Escherichia coli but the number of polymorphic sites was much larger, as could be expected for a more heterogeneous species. Still, as in E. coli, most of the variation found was due to insertions and/or deletions affecting blocks of nucleotides generally located at equivalent regions of the putative secondary structure for both species. Isolated polymorphic sites generated phylogenetic trees generally consistent with the subspecies structure and the accepted relationships among the subspecies. However, the sequences of rrnE put subspecies I closer to E. coli K-12 than to the other S. enterica subspecies. The distribution of polymorphisms affecting blocks of nucleotides was much more random, and the presence of equivalent sequences in distantly related subspecies, and even in E. coli, could reflect relatively frequent horizontal transfer. The smallest 16S-23S spacers in other genera of the family Enterobacteriaceaewere also sequenced. As expected, the level of variation was much larger. Still, the phylogenetic tree inferred is consistent with those of 16S rRNA or housekeeping genes.

Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
Fossil Record ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Charles Darwin ◽  
The Other ◽  
Charles Lyell ◽  
Single Origin ◽  
Molecular Studies ◽  
Richard Owen ◽  
First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

2021 ◽  
pp. 1-8
Author(s):  
Zainab M. Almutairi
Keyword(s):  
Pearl Millet ◽  
Phylogenetic Trees ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Internal Transcribed Spacers ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region ◽  
Local Cultivars ◽  
Pearl Millet Cultivars

Abstract Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

scholarly journals The Eye, the Brain, the Screen – What Neuroscience Can Teach Film Theory

2019 ◽  
Vol 1 (1) ◽  
pp. 1-16
Author(s):  
Paul Elliott
Keyword(s):  
Molecular Biology ◽  
Cultural Theory ◽  
Film Theory ◽  
Mirror Neuron ◽  
The Other ◽  
Perceptual Processing ◽  
Literary Texts ◽  
Cross Model ◽  
The Gaze ◽  
The Brain

“I don’t believe that linguistics and psychoanalysis offer a great deal to the cinema. On the contrary, the biology of the brain – molecular biology – does.” Gilles DeleuzeModels of the brain are inextricably linked to the surrounding cultural episteme: whether it is viewed as a complex clockwork device, a computer, a self-regulating network or even a cinema screen, our understanding of neurophysiology has always relied on discourses and images taken from other fields. In turn, however, our knowledge of cerebral processes (such as sight for instance) has always, inevitably, affected the way that we approach artworks, literary texts and cultural artefacts.Based on this, this paper looks at how recent neuroscientific research on vision and cognition can help us better understand the processes inherent in film theory. Focussing mainly on the recently discovered concept of the mirror neuron but also citing synaesthesia and limbic perceptual processing, I suggest that neuroscience can provide us with a fertile new ground for thinking about areas such as spectatorship and the facilitation of emotional affect, it can also offer us alternatives to monolithic ideas like the Gaze and the patriarchal nature of visual pleasure.Prompted perhaps by a shift in scopic thinking, some recent neuroscientific research has even mirrored film and cultural theory by foregrounding notions such embodiment, cross-model perception and mimesis, adding to the dialogic relationship that exists between these two disciplines. This paper then is not only concerned with how different fields communicate but with how each can provide models, metaphors and frameworks for the other.

scholarly journals Detection, Quantitation, and Phylogenetic Analysis of Noroviruses in Japanese Oysters

2003 ◽  
Vol 69 (10) ◽  
pp. 5782-5786 ◽  
Author(s):  
Tomoko Nishida ◽  
Hirokazu Kimura ◽  
Mika Saitoh ◽  
Michiyo Shinohara ◽  
Masahiko Kato ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Virus Type ◽  
Reverse Transcription ◽  
Real Time Pcr ◽  
The Other ◽  
Capsid Gene ◽  
Neighbor Joining ◽  
Norwalk Virus ◽  
Reverse Transcription Pcr

ABSTRACT Noroviruses (NVs) cause many cases of oyster- or clam-associated gastroenteritis in various countries. We collected 191 samples from Japanese oysters intended for raw consumption that had been harvested from the sea in two different areas between December 2001 and February 2002. To detect, quantitate, and phylogenetically analyze the NV genome in purified concentrates from the stomachs and digestive diverticula of these oysters, we amplified the NV capsid gene by reverse transcription-PCR. Phylogenetic analysis was performed by using the neighbor-joining method. We detected the NV genome in 17 of 191 oysters (9%). Phylogenetic analysis indicated genogroup I (Norwalk virus type) in 3 of the 17 oysters and genogroup II (Snow Mountain virus type) in the other 14. Both genogroups showed wide genetic diversity. To quantify the NV capsid gene in these oysters, we performed real-time PCR using genogroup-specific probes. More than 102 copies of the NV genome were detected in 11 of 17 oysters. The results suggested that about 10% of Japanese oysters intended for raw consumption harbored NVs, and more than 50% of those oysters in which NVs were detected had a large amount.

Verification of Uncurated Protein Annotations

2010 ◽  
pp. 301-314
Author(s):  
Francisco M. Couto ◽  
Mário J. Silva ◽  
Vivian Lee ◽  
Emily Dimmer ◽  
Evelyn Camon ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Molecular Biology ◽  
Domain Knowledge ◽  
Text Processing ◽  
The Other ◽  
Research Projects ◽  
Evidence Text ◽  
Biological Sources ◽  
Biology Research ◽  
Automatic Text

Molecular Biology research projects produced vast amounts of data, part of which has been preserved in a variety of public databases. However, a large portion of the data contains a significant number of errors and therefore requires careful verification by curators, a painful and costly task, before being reliable enough to derive valid conclusions from it. On the other hand, research in biomedical information retrieval and information extraction are nowadays delivering Text Mining solutions that can support curators to improve the efficiency of their work to deliver better data resources. Over the past decades, automatic text processing systems have successfully exploited biomedical scientific literature to reduce the researchers’ efforts to keep up to date, but many of these systems still rely on domain knowledge that is integrated manually leading to unnecessary overheads and restrictions in its use. A more efficient approach would acquire the domain knowledge automatically from publicly available biological sources, such as BioOntologies, rather than using manually inserted domain knowledge. An example of this approach is GOAnnotator, a tool that assists the verification of uncurated protein annotations. It provided correct evidence text at 93% precision to the curators and thus achieved promising results. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

scholarly journals Cystic Echinococcosis: Clinical, Immunological, and Biomolecular Evaluation of Patients from Sardinia (Italy)

Pathogens ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 907
Author(s):  
Cinzia Santucciu ◽  
Piero Bonelli ◽  
Angela Peruzzu ◽  
Alessandro Fancellu ◽  
Vincenzo Marras ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Echinococcus Granulosus ◽  
Cystic Echinococcosis ◽  
Public Health Problem ◽  
Sensu Stricto ◽  
Surgical Removal ◽  
Neighbor Joining ◽  
Intermediate Hosts ◽  
High Prevalence ◽  
Echinococcus Granulosus Sensu Lato

Cystic echinococcosis (CE), a zoonotic disease caused by the larval stage of the tapeworm Echinococcus granulosus sensu lato (s.l.), is a worldwide public health problem. Echinococcus granulosus sensu stricto (s.s.), associated with G1 and G3 genotypes, is endemic with high prevalence in the Mediterranean basin. The parasite’s life cycle comprises definitive hosts (canids) and intermediate hosts (ruminants) and can occasionally involve humans. The main aim of this research was to confirm the diagnosis of 13 patients suspected of CE who presented different complications and needed the surgical removal of the cysts. We also wanted to understand and clarify more the diagnosis of echinococcosis in humans. For this purpose, the patients first underwent cyst evaluation by ultrasound (US), immunological analysis, and then total pericystectomy, followed by parasitological, histopathological, and molecular biology examinations of the cysts. US stadiated one CE1, one CE2, eight CE3b, one CE4, and two CE5; immunology evidenced nine positives; histopathology confirmed 11 CE cysts, of which 8 fertile presenting protoscoleces were identified as E. granulosus s.s. by molecular biology, genotyped as three G1 and four G3 by neighbor-joining (NJ) phylogenetic tree. In conclusion, the results showed that 11 patients were affected by E. granulosus s.s. G1 orG3, and 2 cystic neoformations were of non-parasitic origin.

The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 874-883 ◽  
Author(s):  
Nikolas Nikolaidis ◽  
Zacharias G. Scouras
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Dna Analysis ◽  
Restriction Site ◽  
Species Group ◽  
The Other ◽  
Complex Species ◽  
Restriction Site Maps ◽  
Montium Subgroup

Mitochondrial DNA (mtDNA) restriction site maps for three Drosophila montium subgroup species of the melanogaster species group, inhabiting Indian and Afrotropical montium subgroup territories, were established. Taking into account previous mtDNA data concerning six oriental montium species, a phylogeny was established using distance-matrix and parsimony methods. Both genetic diversity and mtDNA size variations were found to be very narrow, suggesting close phylogenetic relationships among all montium species studied. The phylogenetic trees that were constructed revealed three main lineages for the montium subgroup species studied: one consisting of the Afrotropical species Drosophila seguyi, which is placed distantly from the other species, one comprising the north-oriental (Palearctic) species, and one comprising the southwestern (south-oriental, Australasian, Indian, and Afrotropical) species. The combination of the mtDNA data presented here with data from other species belonging to the melanogaster and obscura subgroups revealed two major clusters: melanogaster and obscura. The melanogaster cluster is further divided into two compact lineages, comprising the montium subgroup species and the melanogaster complex species; the species of the other complex of the melanogaster subgroup, yakuba, disperse among the obscura species. The above grouping is in agreement with the mtDNA size variations of the species. Overall, among all subgroups studied, the species of the montium subgroup seem to be the most closely related. Key words : mtDNA restriction site maps, mtDNA size variations, Drosophila, phylogeny.

Sign in / Sign up

Export Citation Format

Share Document