Genetic and archaeological evidence for a former breeding population of Aleutian Cackling Goose (Branta hutchinsii leucopareia) on Adak Island, central Aleutians, Alaska

2011 ◽  
Vol 89 (8) ◽  
pp. 732-743 ◽  
Author(s):  
B.J. Wilson ◽  
S.J. Crockford ◽  
J.W. Johnson ◽  
R.S. Malhi ◽  
B.M. Kemp
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Dna Sequences ◽  
Archaeological Site ◽  
Breeding Population ◽  
Cytb Gene ◽  
Breeding Ground ◽  
Before Present ◽  
European Contact ◽  
The Past

Many well-preserved bones of medium-sized goose have been recovered from the Zeto Point archaeological site (ADK-011) on Adak Island in the central Aleutians, Alaska, that date to ca. 170–415 years before present based on conventional radiometric dates of the deposits. This prehistoric sample includes remains of adults and unfledged goslings that defied confident identification based on osteological criteria. While the presence of newborns indicates that Adak was a breeding ground, which species was doing the nesting remained uncertain. Of the five species of medium-sized goose (order Anseriformes, family Anatidae) known or presumed to visit Adak Island, three are rarely sighted. The only common visitor is the Emperor Goose ( Chen canagica (Sevastianov, 1802)). The Aleutian Cackling Goose ( Branta hutchinsii leucopareia (Brandt, 1836)) breeds elsewhere in the Aleutians but does not currently breed on Adak Island and there are no records of it nesting there in the past. Here DNA sequences from portions of the cytochrome b (cytb) gene and the control region (CR) of the mitochondrial genome were recovered from 28 of 29 Adak prehistoric goose remains. All adult specimens identified to species were either C. canagica or B. h. leuopareia, but all specifically identified juvenile specimens were B. h. leuopareia. The results demonstrate that Adak Island was a breeding ground of the Aleutian Cackling Goose prior to European contact.

scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

Detection of Flaviviral-Like DNA Sequences in Aedes aegypti (Diptera: Culicidae) Collected From Argentina

2021 ◽  
Author(s):  
Melisa B Bonica ◽  
Dario E Balcazar ◽  
Ailen Chuchuy ◽  
Jorge A Barneche ◽  
Carolina Torres ◽  
...  
Keyword(s):  
Public Health ◽  
Aedes Aegypti ◽  
Dna Sequences ◽  
Immature Stages ◽  
Public Health Burden ◽  
The Past ◽  
Health Burden ◽  
The World ◽  
Aegypti Genome ◽  
Dengue Epidemics

Abstract Diseases caused by flaviviruses are a major public health burden across the world. In the past decades, South America has suffered dengue epidemics, the re-emergence of yellow fever and St. Louis encephalitis viruses, and the introduction of West Nile and Zika viruses. Many insect-specific flaviviruses (ISFs) that cannot replicate in vertebrate cells have recently been described. In this study, we analyzed field-collected mosquito samples from six different ecoregions of Argentina to detect flaviviruses. We did not find any RNA belonging to pathogenic flaviviruses or ISFs in adults or immature stages. However, flaviviral-like DNA similar to flavivirus NS5 region was detected in 83–100% of Aedes aegypti (L.). Despite being previously described as an ancient element in the Ae. aegypti genome, the flaviviral-like DNA sequence was not detected in all Ae. aegypti samples and sequences obtained did not form a monophyletic group, possibly reflecting the genetic diversity of mosquito populations in Argentina.

scholarly journals Data Structures to Represent a Set of k -long DNA Sequences

2021 ◽  
Vol 54 (1) ◽  
pp. 1-22
Author(s):  
Rayan Chikhi ◽  
Jan Holub ◽  
Paul Medvedev
Keyword(s):  
Data Structures ◽  
Dna Sequences ◽  
Sequencing Data ◽  
String Algorithms ◽  
Fixed Length ◽  
The Past

The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k -mers, which are short fixed-length strings present in a dataset. While these approaches are rather diverse, storing and querying a k -mer set has emerged as a shared underlying component. A set of k -mers has unique features and applications that, over the past 10 years, have resulted in many specialized approaches for its representation. In this survey, we give a unified presentation and comparison of the data structures that have been proposed to store and query a k -mer set. We hope this survey will serve as a resource for researchers in the field as well as make the area more accessible to researchers outside the field.

scholarly journals Sequência estratigráfica e materiais cerâmicos do sítio da Póvoa do Mileu (Guarda, Portugal) = Stratigraphic sequence and ceramic materials of the settlement of Póvoa do Mileu (Guarda, Portugal)

2020 ◽  
pp. 135
Author(s):  
Vitor Manuel Fernandes Pereira ◽  
Tiago Pinheiro Ramos
Keyword(s):  
Roman Empire ◽  
Archaeological Site ◽  
Ceramic Materials ◽  
Archaeological Sites ◽  
Local Production ◽  
Stratigraphic Sequence ◽  
Trade Routes ◽  
The Past ◽  
Historic City ◽  
Railroad Station

<p>Accidentalmente descubierto en 1951, durante la construcción de la carretera de enlace entre la ciudad histórica y la estación de ferrocarril, el yacimiento arqueológico de Mileu se convirtió rápidamente en uno de los yacimientos arqueológicos más emblemáticos de la Beira Interior. En este artículo, tenemos la intención de presentar<br />los resultados de la investigación que hemos desarrollado en el sitio en los últimos 15 años, destacando el análisis del material cerámico como elemento de datación de las diferentes fases de ocupación de Mileu. Su análisis confirma una secuencia ocupacional desde la primera mitad del siglo I A.D hasta los siglos XII / XIII. Los materiales romanos analizados son principalmente de importación, permitiendo no solo una datación de contextos, sino también comprender su origen, el contexto de su uso o cuestiones relacionadas con las rutas comerciales dentro del Imperio Romano y el cruce del territorio de la Beira Interior. En cuanto a los materiales medievales, de producción local, muestran la continuación de la ocupación del yacimiento en épocas pos-romana</p><p>Accidentally discovered in 1951, during the construction of the link road between the historic city and the railroad station, the archaeological site of Mileu quickly became one of the most emblematic archaeological sites of Beira Interior. In this article we plan to present the results of research that we have developed on the site over the past<br />15 years, highlighting the analysis of the ceramic material while dating element of the different occupation phases of Mileu. Their analysis confirms an occupational sequence from the first half of the century A.D. to the XII / XIII centuries. The analyzed Roman materials are primarily imported, allowing not only a dating of contexts, but also how to understand their origin, the context of its use, or issues related to the trade routes within the Roman Empire and crossing the territory of Beira Interior. As for the medieval materials, local production, show the continuation of the occupation site in post-Roman times</p>

scholarly journals Numerical simulation of a sinking ship scenario based on archaeological records

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Smiljko Rudan ◽  
Irena Radić Rossi
Keyword(s):  
Numerical Simulation ◽  
System Dynamics ◽  
Archaeological Site ◽  
3D Modelling ◽  
Body System ◽  
Standard Practice ◽  
The Past ◽  
Modern Engineering ◽  
The Creation ◽  
Multi Body

Over the past decade, photogrammetric recording and virtual 3D modelling have evolved as a standard practice in documenting shipwreck sites. Exploiting the same methods, we can attempt to virtually reconstruct the dynamics of an accident leading to the creation of an archaeological site. By applying modern engineering tools capable of deploying multi-body system dynamics to simulate the damaging, capsizing and/or sinking of a ship, we can model and analyse the various possible scenarios of an incident occurring to an ancient merchantman. Subsequently, we can establish the correlation between the characteristics of the actual shipwreck site, and the outcome of the numerical simulation of the assumed scenario.

scholarly journals Altitude-wise analysis of co-occurrence networks of mitochondrial genome in Asian population

2019 ◽  
Author(s):  
Rahul K Verma ◽  
Cristina Giuliani ◽  
Alena Kalyakuina ◽  
Ajay Deep Kachhvah ◽  
Mikhail Ivanchenko ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
High Altitude ◽  
Dna Sequences ◽  
Group Analysis ◽  
Asian Population ◽  
The Tibetan Plateau ◽  
Mt Dna ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
The Impact

ABSTRACTFinding mechanisms behind high altitude adaptation in humans at the Tibetan plateau has been a subject of evolutionary research. Mitochondrial DNA (mt-DNA) variations have been established as one of the key players in understanding the biological mechanisms at the basis of adaptation to these extreme conditions. To explore cumulative effects and dynamics of the variations in mitochondrial genome at varying altitudes, we investigated human mt-DNA sequences from NCBI database at different altitudes by employing co-occurrence motifs framework. We constructed co-occurrence motifs by taking into account variable sites for each altitude group. Analysis of the co-occurrence motifs using similarity clustering revealed a clear distinction between a lower and a higher altitude region. In addition, the previously known high altitude markers 3394 and 7697 (which are definitive sites of haplogroup M9a1a1c1b) were found to co-occur within their own gene complexes indicating the impact of intra-genic constraint on co-evolution of nucleotides. Furthermore, an ancestral marker 10398 was found to co-occur only at higher altitudes supporting the fact that a separate root of colonization at these altitudes might have taken place. Overall, our analysis revealed the presence of co-occurrence motifs at a whole mitochondrial genome level. This study, combined with the classical haplogroups analysis is useful in understanding role of co-occurrence of mitochondrial variations in high altitude adaptation.

An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion

Gene ◽  
2015 ◽  
Vol 573 (2) ◽  
pp. 216-224 ◽  
Author(s):  
Xidong Mu ◽  
Xuejie Wang ◽  
Yi Liu ◽  
Hongmei Song ◽  
Chao Liu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Structure ◽  
Coding Region
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