DNA polymorphism of dogs (Canis familiaris L.). I. Origin, distribution of dogs in the light of molecular biological data about their mitochondrial and nuclear genomes

Biomics ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 298-308
Author(s):  
D.A. Chemeris ◽  
Yu.R. Giniyatov ◽  
R.R. Garafutdinov ◽  
A.V. Chemeris
Keyword(s):  
Western Europe ◽  
Dna Polymorphism ◽  
Nuclear Dna ◽  
Canis Familiaris ◽  
Biological Data ◽  
Migration Routes ◽  
Points Of View ◽  
Nuclear Genomes ◽  
Biological Methods ◽  
Mtdna Polymorphism

Information is given on the size and organization of the mitochondrial and nuclear genomes of dogs, including information on polymorphisms of some loci used to clarify the phylogenetic relationships of wolves and the first dogs, including hypotheses about the places of domestication of ancient now extinct wolves and the dates of these events. It is noted that the introduction of molecular biological methods in archaeology has allowed to obtain the principally new data on ancient wolves and dogs. Based on mtDNA polymorphism and nuclear DNA polymorphism, migration routes of already domesticated dogs together with humans have been tracked. The previously existing points of view about the origin of the first dogs in Western Europe, as well as in East Asia, have been supplemented in recent years by assumptions about the appearance of the first proto-dogs in Siberia.

scholarly journals Cryptic speciation in the Warbling Vireo (Vireo gilvus)

The Auk ◽  
2021 ◽  
Author(s):  
Scott F Lovell ◽  
M Ross Lein ◽  
Sean M Rogers
Keyword(s):  
Contact Zone ◽  
Nuclear Dna ◽  
Biological Species ◽  
Valid Species ◽  
Migration Routes ◽  
Dna Evidence ◽  
Show Evidence ◽  
And Migration ◽  
Surrounding Areas ◽  
Taxonomic Groups

Abstract Eastern (Vireo gilvus gilvus) and western (V. g. swainsoni) forms of the Warbling Vireo have essentially allopatric breeding ranges across north-central North America, but come into contact in central Alberta, Canada. In 1986, Jon Barlow presented preliminary morphological and song evidence suggesting that the Warbling Vireo complex might comprise more than one valid species. However, to date, Barlow’s suggestion is supported by only limited DNA evidence, demonstration of molt and migration differences between the taxa, and anecdotal accounts of differences in song, morphology, plumage, and ecology. We analyzed variation in both mitochondrial and nuclear DNA in birds from Alberta and surrounding areas to determine the levels of genetic differentiation and hybridization occurring in the contact zone, and whether the two taxa warrant recognition as separate biological species. Our analyses reveal that Warbling Vireos in Alberta and the surrounding areas are separated into two well-defined, genetically differentiated, and monophyletic clades corresponding to previously recognized taxonomic groups. The two taxa come into contact in a narrow (~85 km) zone in Barrhead County, northwest of Edmonton, Alberta. They show evidence of limited hybridization. The distinct genetic differences are maintained in the contact zone, where individuals of the two taxa may occupy neighboring territories. Differences in spring arrival dates, molt schedules, and migration routes indicate that a migratory divide may play an important role in reproductive isolation. We suggest that the two taxa are distinct cryptic species: an eastern form, Vireo gilvus, and a western form, Vireo swainsoni.

scholarly journals Morphological and genetic differentiation of Bufo toads: two cryptic species in Western Europe (Anura, Bufonidae)

2013 ◽  
Vol 82 (4) ◽  
pp. 147-169 ◽  
Author(s):  
Jan W. Arntzen ◽  
Jacob McAtear ◽  
Ernesto Recuero ◽  
Janine M. Ziermann ◽  
Annemarie Ohler ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Western Europe ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Bufo Bufo ◽  
Sensu Stricto ◽  
Additional Species ◽  
Morphometric Characters ◽  
Evolutionary Context

The Common toad Bufo bufo sensu lato is a widespread, morphologically conserved taxon. Recent studies have uncovered deep genetic differentiation between population groups, highlighting the need to revise the current taxonomy of the group and recognize additional species. Here we investigate patterns of variation in molecular (a mitochondrial DNA restriction enzyme assay and sequence data for two nuclear DNA fragments totalling 979 bp) and 17 morphological variables in Northern France where two of these groups meet (B. bufo sensu stricto and B. spinosus), in order to delineate their contact zone and uncover characters that would allow discrimination of the two taxa. Mitochondrial DNA data show an abrupt transition from areas where B. bufo is present to those inhabited by B. spinosus, with a narrow area of overlap east of the city of Caen. Morphometric characters, particularly those related to the positioning of the parotoid glands and metatarsal tubercle shape and size, proved useful in discriminating between species (AUC ≥ 0.97, kappa ≥ 0.79). We then used the differentiating character states to allocate over 300 museum specimens from Western Europe to either species with consistent results, including comparable values of AUC and kappa of the identification models, indicating that models could successfully be applied across datasets. We summarize available evidence relevant to the delineation of the distribution of B. bufo and B. spinosus in France and discuss the characters differentiating both species in an evolutionary context. In view of the observed morphological and genetic differentiation and the absence of unequivocal evidence for widespread hybridization we support the view that B. bufo and B. spinosus are best considered different species. Finally, we propose that ‘parotoids in parallel position’ and a thin and smooth skin are derived character states for B. bufo over the northern part of its range.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Sub Saharan Africa ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

The Wayward Dog: Is the Australian native dog or Dingo a distinct species?

Zootaxa ◽  
2017 ◽  
Vol 4317 (2) ◽  
pp. 201 ◽  
Author(s):  
STEPHEN M. JACKSON ◽  
COLIN P. GROVES ◽  
PETER J.S. FLEMING ◽  
KEN P. APLIN ◽  
MARK D.B. ELDRIDGE ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Canis Familiaris ◽  
Distinct Species ◽  
Biological Data ◽  
Zoological Nomenclature ◽  
Morphological Evidence ◽  
Recent Proposal ◽  
Initial Description ◽  
Free Ranging ◽  
Scientific Name

The taxonomic identity and status of the Australian Dingo has been unsettled and controversial since its initial description in 1792. Since that time it has been referred to by various names including Canis dingo, Canis lupus dingo, Canis familiaris and Canis familiaris dingo. Of these names C. l. dingo and C. f. dingo have been most often used, but it has recently been proposed that the Australian Dingo should be once again recognized as a full species—Canis dingo. There is an urgent need to address the instability of the names referring to the Dingo because of the consequences for management and policy. Therefore, the objective of this study was to assess the morphological, genetic, ecological and biological data to determine the taxonomic relationships of the Dingo with the aim of confirming the correct scientific name. The recent proposal for Canis dingo as the most appropriate name is not sustainable under zoological nomenclature protocols nor based on the genetic and morphological evidence. Instead we proffer the name C. familiaris for all free-ranging dogs, regardless of breed and location throughout the world, including the Australian Dingo. The suggested nomenclature also provides a framework for managing free-ranging dogs including Dingoes, under Australian legislation and policy. The broad principles of nomenclature we discuss here apply to all free-roaming dogs that coexist with their hybrids, including the New Guinea Singing Dog. 

PATH-BASED SYSTEMS TO GUIDE SCIENTISTS IN THE MAZE OF BIOLOGICAL DATA SOURCES

2006 ◽  
Vol 04 (05) ◽  
pp. 1069-1095 ◽  
Author(s):  
SARAH COHEN-BOULAKIA ◽  
SUSAN DAVIDSON ◽  
CHRISTINE FROIDEVAUX ◽  
ZOÉ LACROIX ◽  
MARIA-ESTHER VIDAL
Keyword(s):  
Biological Data ◽  
Data Sources ◽  
Single Experiment ◽  
Novel Technologies ◽  
Biological Resources ◽  
Wet Lab ◽  
Points Of View ◽  
Growing Network ◽  
The Way

Fueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer. Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data. In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.

scholarly journals The ubiquitous potential Z-forming sequence of eucaryotes, (dT-dG)n . (dC-dA)n, is not detectable in the genomes of eubacteria, archaebacteria, or mitochondria.

1986 ◽  
Vol 6 (8) ◽  
pp. 3010-3013 ◽  
Author(s):  
D S Gross ◽  
W T Garrard
Keyword(s):  
Sequence Analysis ◽  
Nuclear Dna ◽  
Repeat Element ◽  
Phylogenetic Distribution ◽  
Base Pairs ◽  
Nuclear Genomes

The potential Z-forming sequence (dT-dG)n . (dC-dA)n is an abundant, interspersed repeat element that is ubiquitous in eucaryotic nuclear genomes. We report that in contrast to eucaryotic nuclear DNA, the genomes of eubacteria, archaebacteria, and mitochondria lack this sequence, since even a single tract of greater than or equal to 14 base pairs in length is not detectable through either hybridization or sequence analysis. Interestingly, the phylogenetic distribution of the (dT-dG)n . (dC-dA)n repeat exhibits a striking parallel to that of (dT-dC)n . (dG-dA)n, but not to other homocopolymeric sequences such as (dC-dG)n . (dC-dG)n or (dT-dA)n . (dT-dA)n.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

2019 ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes ◽  
Generation Sequencing

Abstract Background: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

scholarly journals THE IMAGEIS OF GERMAN CITIES IN RUSSIAN TRAVELOGUES AT THE TURN OF XIX CENTURY

2017 ◽  
pp. 189-194
Author(s):  
S. S. Zhdanov
Keyword(s):  
Western Europe ◽  
Cultural Artifacts ◽  
Self Identity ◽  
Figures Of Speech ◽  
Space Limitation ◽  
Points Of View ◽  
Xix Century ◽  
German Cities

The  paper  deals  with  specific  features  of  representing  German  cities and towns   in   Russian   travelogues   at   the   turn   of   the   XIX century   written by V. N. Zinov'ev,  D. I. Fonvizin,  N. M. Karamzin  and  F. P. Lubyanovskiy.  These texts reflect pursuance of Russian self-identity on the basis of comparison with Western Europe, in particular, with Germany. The Russian authors focus on culturespecific elements of the represented locuses. Cleanness, comfort, space limitation and closeness should also be mentioned as characteristics of the German urban chronotopos. The urban locus is represented from two points of view: as a space of cultural artifacts and as an anthropic space of citizens. The second aspect is important for N. M. Karamzin and F. P. Lubyanovskiy’s sentimentalistic texts but can hardly be found  in  works  by  V. N. Zinov'ev  and  D. I. Fonvizin.  The  urban  descriptions in sentimentalists’ travelogues are more voluminous, filled with figures of speech, different historic and contemporaneous realia. 

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

2019 ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes ◽  
Generation Sequencing

Abstract Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

scholarly journals Archaic mitochondrial DNA inserts in modern day nuclear genomes

2019 ◽  
Author(s):  
Robert Bücking ◽  
Murray P Cox ◽  
Georgi Hudjashov ◽  
Lauri Saag ◽  
Herawati Sudoyo ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Dna ◽  
Modern Human ◽  
Next Generation Sequencing Data ◽  
Human Populations ◽  
Sequencing Data ◽  
Modern Humans ◽  
High Coverage ◽  
Nuclear Genomes ◽  
Generation Sequencing

Abstract Background: Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Sahara Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results: We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions: Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.

Sign in / Sign up

Export Citation Format

Share Document