scholarly journals Unsupervized Quantification of Demographic Structure for Single-copy Alignments

2018 ◽  
Author(s):  
AB Rohrlach ◽  
Nigel Bean ◽  
Gary Glonek ◽  
Barbara Holland ◽  
Ray Tobler ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Sequence Alignments ◽  
Genetic Studies ◽  
Single Copy Sequence ◽  
Copy Sequence ◽  
Quantitative Characteristics ◽  
Source Of Information ◽  
Qualitative And Quantitative Characteristics

AbstractSingle-copy sequence alignments have been a valuable source of information for genetic studies; their lack of recombination makes phylogenetic analyses tractable [1]. Specifically, mitochondrial DNA will continue to play an important role in genetic studies due to its high mutation rate and high copy per cell count of the molecule [2]. In this paper we develop a new method for the analysis of single-copy sequence data that simultaneously considers the relationships between sequenced individuals and positions of interest in the genome. We then show that tests for relationships between genetic information and qualitative and quantitative characteristics can be calculated. We motivate the use of our method with examples from empirical data.

Characterization and evolution of a single-copy sequence from the human Y chromosome

1985 ◽  
Vol 5 (3) ◽  
pp. 576-581
Author(s):  
R D Burk ◽  
P Ma ◽  
K D Smith
Keyword(s):  
Y Chromosome ◽  
Primate Evolution ◽  
Single Copy ◽  
Homologous Sequence ◽  
Old World Monkeys ◽  
Chromosomal Distribution ◽  
Human Dna ◽  
Single Copy Sequence ◽  
Copy Sequence ◽  
Human Y Chromosome

To study the evolution and organization of DNA from the human Y chromosome, we constructed a recombinant library of human Y DNA by using a somatic cell hybrid in which the only cytologically detectable human chromosome is the Y. One recombinant (4B2) contained a 3.3-kilobase EcoRI single-copy fragment which was localized to the proximal portion of the Y long arm. Sequences homologous to this human DNA are present in male gorilla, chimpanzee, and orangutan DNAs but not in female ape DNAs. Under stringent hybridization conditions, the homologous sequence is either a single-copy or a low-order repeat in humans and in the apes. With relaxed hybridization conditions, this human Y probe detected several homologous DNA fragments which are all derived from the Y in that they occur in male DNAs from humans and the apes but not in female DNAs. In contrast, this probe hybridized to highly repeated sequences in both male and female DNAs from old world monkeys. Thus, sequences homologous to this probe underwent a change in copy number and chromosomal distribution during primate evolution.

scholarly journals An arbitrary single copy sequence VC64 [D1S86] detects a moderate frequency TaqI RFLP on chromosome 1

1989 ◽  
Vol 17 (10) ◽  
pp. 4009-4009
Author(s):  
Vera Verga ◽  
Maria Dos Santos ◽  
Isabelle Marques ◽  
Sue Povey ◽  
Michele Ramsay ◽  
...  
Keyword(s):  
Single Copy ◽  
Chromosome 1 ◽  
Moderate Frequency ◽  
Single Copy Sequence ◽  
Copy Sequence

Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates

1994 ◽  
Vol 39 (4) ◽  
pp. 331-339 ◽  
Author(s):  
Simone Cacci� ◽  
Paolo Perani ◽  
Salvatore Saccone ◽  
Farida Kadi ◽  
Giorgio Bernardi
Keyword(s):  
Sequence Homology ◽  
Single Copy ◽  
Single Copy Sequence ◽  
Copy Sequence

scholarly journals A TaqI RFLP demonstrated for pIBS17 [D4S123], a single copy sequence on chromosome 4

1988 ◽  
Vol 16 (6) ◽  
pp. 2743-2743
Author(s):  
L.D. Berdahl ◽  
R.F. Smith ◽  
J.C. Murray ◽  
K.H. Buetow
Keyword(s):  
Single Copy ◽  
Chromosome 4 ◽  
Single Copy Sequence ◽  
Copy Sequence

The Gene Coding for Tropoelastin is Represented as a Single Copy Sequence in the Haploid Sheep Genome

1987 ◽  
Vol 7 (1) ◽  
pp. 77-89 ◽  
Author(s):  
Louise Olliver ◽  
Phyllis A. Luvalle ◽  
Jeffrey M. Davidson ◽  
Joel Rosenbloom ◽  
Christopher G. Mathew ◽  
...  
Keyword(s):  
Single Copy ◽  
Sheep Genome ◽  
Gene Coding ◽  
Single Copy Sequence ◽  
Copy Sequence

Phylogeny of Trematomus (Notothenioidei: Nototheniidae) inferred from mitochondrial and nuclear gene sequences

2009 ◽  
Vol 21 (6) ◽  
pp. 565-570 ◽  
Author(s):  
Kristen L. Kuhn ◽  
Thomas J. Near
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Single Copy ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Phylogenetic Resolution

AbstractThe biota of Antarctica is amazingly rich and highly endemic. The phylogenetics of notothenioid fishes has been extensively investigated through analyses of morphological characters, DNA sequences from mitochondrial genes, and single copy nuclear genes. These phylogenetic analyses have produced reasonably similar phylogenetic trees of notothenioids, however a number of phylogenetic questions remain. The nototheniid clade Trematomus is an example of a group where phylogenetic relationships remain unresolved. In this paper we revisit the phylogenetic relationships of Trematomus using both increased taxon sampling and an expanded dataset which includes DNA sequences from two mitochondrial genes (ND2 and 16S rRNA) and one single-copy nuclear gene (RPS7). The Bayesian phylogeny resulting from the analysis of the combined mitochondrial and nuclear gene datasets was well resolved and contained more interspecific nodes supported with significant Bayesian posteriors than either the mitochondrial or nuclear gene phylogenies alone. This demonstrates that the addition of nuclear gene sequence data to mitochondrial data can enhance phylogenetic resolution and increase node support. Additionally, the results of the combined mitochondrial and nuclear Bayesian analyses provide further support for the inclusion of species previously classified as Pagothenia and Cryothenia in Trematomus.

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