Correlation of Functional Domains and Rates of Nucleotide Substitution in Cytochromeb

Griffiths, Carole S.

doi:10.1006/mpev.1997.0404

Cited by 117 publications

(61 citation statements)

References 49 publications

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“…In evaluating recombination, it is instructive to ask whether nonrecombining sequences can show similar bootscan and pairwise distances as those obtained previously with subtype E sequences. Differences in the rates of evolution or substitution across the genome can potentially confound phylogenetic signal (15,16). To address this issue, we simulated multiple nucleotide alignments corresponding to the 36 complete genome sequences (alignment 2) used in our bootscanning and pairwise distance analyses.…”

Section: Methodsmentioning

confidence: 99%

Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E

Anderson¹,

Rodrigo

Learn

et al. 2000

J Virol

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The human immunodeficiency virus type 1 (HIV-1) epidemic in Southeast Asia has been largely due to the emergence of clade E (HIV-1E). It has been suggested that HIV-1E is derived from a recombinant lineage of subtype A (HIV-1A) and subtype E, with multiple breakpoints along the E genome. We obtained complete genome sequences of clade E viruses from Thailand (93TH057 and 93TH065) and from the Central African Republic (90CF11697 and 90CF4071), increasing the total number of HIV-1E complete genome sequences available to seven. Phylogenetic analysis of complete genomes showed that subtypes A and E are themselves monophyletic, although together they also form a larger monophyletic group. The apparent phylogenetic incongruence at different regions of the genome that was previously taken as evidence of recombination is shown to be not statistically significant. Furthermore, simulations indicate that bootscanning and pairwise distance results, previously used as evidence for recombination, can be misleading, particularly when there are differences in substitution or evolutionary rates across the genomes of different subtypes. Taken jointly, our analyses suggest that there is inadequate support for the hypothesis that subtype E variants are derived from a recombinant lineage. In contrast, many other HIV strains claimed to have a recombinant origin, including viruses for which only a single parental strain was employed for analysis, do indeed satisfy the statistical criteria we propose. Thus, while intersubtype recombinant HIV strains are indeed circulating, the criteria for assigning a recombinant origin to viral structures should include statistical testing of alternative hypotheses to avoid inappropriate assignments that would obscure the true evolutionary properties of these viruses.

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Section: Methodsmentioning

confidence: 99%

Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E

Anderson¹,

Rodrigo

Learn

et al. 2000

J Virol

View full text Add to dashboard Cite

show abstract

“…SeqEd v1.0.3 (Applied Biosystems) was utilized to identify amino acid substitutions. We assessed levels of saturation for our data set of mtDNA genes by plotting corrected pairwise distances with numbers of transitions and transversions among species (Brown, 1983;Griffiths, 1997).…”

Section: Molecular Characterization and Phylogenetic Analysismentioning

confidence: 99%

Molecular systematics and biogeography of the Neotropical monkey genus, Alouatta

Cortés‐Ortiz

Bermingham

Rico

et al. 2003

Molecular Phylogenetics and Evolution

284

193

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“…The aim of the present study was to clarify the scientific name, to clear the confusion surrounding the taxonomic status of the Korean collared scops owl, and to provide basic information for its conservation. We also sought to verify relationships among the three Otus species using mitochondrial cyt b, which has been used for owl systematic classification (Heidrich et al, 1995;Griffiths, 1997;Mindell et al, 1997;Ryu and Park, 2003;Wink et al, 2004), and additional ND2 sequences. All the ML, MP, and NJ trees of both regions (cyt b and ND2) confirmed that the Korean species is clearly different from O. lempiji and O. bakkamoena, which are the scientific names used officially for the collared scops owl in Korea.…”

Section: Discussionmentioning

confidence: 99%

Determining the Specific Status of Korean Collared Scops Owls

Hong¹,

Kim²,

Murata³

et al. 2013

Animal Systematics, Evolution and Diversity

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The collared scops owl that occurs in Korea is a protected species but its exact specific status has been questioned. To resolve the species status, a molecular phylogenetic analysis was conducted using two fragments of mitochondrial DNA, cytochrome b (cyt b, 891 bp) and NADH dehydrogenase subunit 2 (ND2, 627 bp) genes. Phylogenetic trees of cyt b revealed that all Korean specimens formed a monophyletic group with Japanese scops owl Otus semitorques with very low sequence divergence (d= =0.008). We obtained a similar ND2 tree as well (d= =0.003); however, the genetic distance between Korean individuals and O. lempiji from GenBank (AJ004026-7, EU348987, and EU601036) was very high and sufficient enough to separate them as species (cyt b, d= =0.118; ND2, d= =0.113). We also found that Korean species showed high differentiation from O. bakkamoena (AJ004018-20 and EU601034; cyt b, d= =0.106; ND2, d= =0.113) and O. lettia (EU601109 and EU601033, cyt b, d= =0.110; ND2, d= =0.117) as well. Therefore, we suggest that the Korean collared scops owl should be designated as Otus semitorques.

show abstract

Correlation of Functional Domains and Rates of Nucleotide Substitution in Cytochromeb

Cited by 117 publications

References 49 publications

Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E

Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E

Molecular systematics and biogeography of the Neotropical monkey genus, Alouatta

Determining the Specific Status of Korean Collared Scops Owls

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