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Molecular phylogeny
“Of outstanding in the opinion Authors year’s selection 1991 Gene
of geneticists
interest” and developmental
biologists.
of reviews in the Current Opinion series of journals select from the previous papers those they consider to be “of outstanding interest”. They justify each in a short ‘annotation’. Some of the selected references from the December issue of Current Opinion in Genetics and Development, which covers both Organization and Evolution, are listed below under the titles of the reviews.
Molecular phylogeny Barbara H. Bowman
by Arend Sidow and
The limitedl universe of exons by Robert L. Dorit and Walter Gilbert
KLWINO H, MIYATA T, HASEGAWA M: Maximum Likelihood Inference of Protein Phylogeny and the Origin of Chloroplasts. J lclol Evol 1990, 31:151-160. A must. This paper is very clearly written and emphasizes
the importance of proper methodology. (Do not be deterred by the math.) The authors present a maximumlikelihood method for phylogenetic analysis of protein sequences, based on a Markov model for amino acid substitutions (although a rate matrix more advanced than Dayhoffs might be used in the future). Support is presented for excluding the prochlorophyte Procblorothrix bollund&2 as a car&late for the closest relative of plant chloroplasts.
Early evolution and the origin Mitchell L. Sogin
of eukaryotes
by
PATIHY L: Modular
Exchange Principles in Proteins. Curr Opin Struct Biol 1991, 3:351361.
A comprehensive review of most of the recently uncovered instances of exon shuffling The author also empha sizes certain empirical regularities about domains that are likely to be involved in shufFling events, such as beginning and ending phase. LUTHY R, MCI&HAN AD, EISENBERG D: Secondary Structure-based ProNes: Use of Structure-conserv-
ing Scoring Tables in Searching Protein Sequence Databases for Structural Similarities. Proteins 1991, 10:229-239. An important extension of the profile method for identi@ing distantly related protein sequences. The authors incorporate information from known protein secondary structures and develop a weighting matrix that can detect structural similarities in cases where sequence simiiarily has been lost.
GAJADHARAA, ~~ARQUARDT WC, HALL R, GL~VDERSON J, ARLZTL&ARMONAEV, SOGIN ML: Evolutionary Rela-
tionships among Apkomplexans, Dinoflagellates, and Ciliates: Ribosomal RNA Sequences of Surcocystis murk, Tbeileria annulata and Crypthecodinium cohnii. Mel Biochem: Parasitol 1991, 45:147-154.
RNA viruses: genome structure and evolution by Ellen G. Strauss and James H. Strauss
Similarities between subunit rRNA sequences demonstrate that dino&geU,ates and apicomplexans are sister groups which share a common evolut.ionaIy history with ciliated protozoa. These phyla delineate a fifth complex evolutionary assemblage (animals, plants, fungi, and oomycetes/chromophyte algae define the other four major complex evolutionary assemblages) within the eukaryotic kingdom. These groups diverged from each other during a relatively short period approximately 1 btilion years ago.
Bovine Paminfluenza Virus 3 Expresses alI Three Reading Frames From a Single m.RNA Editing Site. EMBOJ 1991, 10:443-448.
PELET T, CURRANJ, KOLAKOVSKY D: The P Gene of
A comprehensive look at all of the mRNA transcripts and translated protein products of the P gene of PIV-3, illustrating that all three reading frames are used over a stretch of more than 300 nucleotides. This may be the first gene sequenced in which all three frames are used. SNIJDER EJ, DEN Boon
JA, HOFLZINEK MC, SPAAN WJM:
BUTTERFIELDNJ, KNOIL AH, SW?T K: A Bangiophyte Red Alga from the Proterozoic of Arctic Canada. Science 1990, 250~10~107.
of the Genome Organization of Toroand Coronaviruses: Evidence for Two Nonhomologous RNA Recombination Events During Berne Virus Evolution. ViroZoa 1991, 180:448452.
Evidence of 1.25 million year old multicellular algae is presented, raising the possibility that photosynthetic eukalyotes inhabited the earth two biion years ago.
Sequence analysis to suggest that coronaviruses and toroviruses are related and that recombtition has played a role in their evolution.
Comparison
Volume 2
Number 1
1992
33
of geneticists
interest” and developmental
biologists.
of reviews in the Current Opinion series of journals select from the previous papers those they consider to be “of outstanding interest”. They justify each in a short ‘annotation’. Some of the selected references from the December issue of Current Opinion in Genetics and Development, which covers both Organization and Evolution, are listed below under the titles of the reviews.
Molecular phylogeny Barbara H. Bowman
by Arend Sidow and
The limitedl universe of exons by Robert L. Dorit and Walter Gilbert
KLWINO H, MIYATA T, HASEGAWA M: Maximum Likelihood Inference of Protein Phylogeny and the Origin of Chloroplasts. J lclol Evol 1990, 31:151-160. A must. This paper is very clearly written and emphasizes
the importance of proper methodology. (Do not be deterred by the math.) The authors present a maximumlikelihood method for phylogenetic analysis of protein sequences, based on a Markov model for amino acid substitutions (although a rate matrix more advanced than Dayhoffs might be used in the future). Support is presented for excluding the prochlorophyte Procblorothrix bollund&2 as a car&late for the closest relative of plant chloroplasts.
Early evolution and the origin Mitchell L. Sogin
of eukaryotes
by
PATIHY L: Modular
Exchange Principles in Proteins. Curr Opin Struct Biol 1991, 3:351361.
A comprehensive review of most of the recently uncovered instances of exon shuffling The author also empha sizes certain empirical regularities about domains that are likely to be involved in shufFling events, such as beginning and ending phase. LUTHY R, MCI&HAN AD, EISENBERG D: Secondary Structure-based ProNes: Use of Structure-conserv-
ing Scoring Tables in Searching Protein Sequence Databases for Structural Similarities. Proteins 1991, 10:229-239. An important extension of the profile method for identi@ing distantly related protein sequences. The authors incorporate information from known protein secondary structures and develop a weighting matrix that can detect structural similarities in cases where sequence simiiarily has been lost.
GAJADHARAA, ~~ARQUARDT WC, HALL R, GL~VDERSON J, ARLZTL&ARMONAEV, SOGIN ML: Evolutionary Rela-
tionships among Apkomplexans, Dinoflagellates, and Ciliates: Ribosomal RNA Sequences of Surcocystis murk, Tbeileria annulata and Crypthecodinium cohnii. Mel Biochem: Parasitol 1991, 45:147-154.
RNA viruses: genome structure and evolution by Ellen G. Strauss and James H. Strauss
Similarities between subunit rRNA sequences demonstrate that dino&geU,ates and apicomplexans are sister groups which share a common evolut.ionaIy history with ciliated protozoa. These phyla delineate a fifth complex evolutionary assemblage (animals, plants, fungi, and oomycetes/chromophyte algae define the other four major complex evolutionary assemblages) within the eukaryotic kingdom. These groups diverged from each other during a relatively short period approximately 1 btilion years ago.
Bovine Paminfluenza Virus 3 Expresses alI Three Reading Frames From a Single m.RNA Editing Site. EMBOJ 1991, 10:443-448.
PELET T, CURRANJ, KOLAKOVSKY D: The P Gene of
A comprehensive look at all of the mRNA transcripts and translated protein products of the P gene of PIV-3, illustrating that all three reading frames are used over a stretch of more than 300 nucleotides. This may be the first gene sequenced in which all three frames are used. SNIJDER EJ, DEN Boon
JA, HOFLZINEK MC, SPAAN WJM:
BUTTERFIELDNJ, KNOIL AH, SW?T K: A Bangiophyte Red Alga from the Proterozoic of Arctic Canada. Science 1990, 250~10~107.
of the Genome Organization of Toroand Coronaviruses: Evidence for Two Nonhomologous RNA Recombination Events During Berne Virus Evolution. ViroZoa 1991, 180:448452.
Evidence of 1.25 million year old multicellular algae is presented, raising the possibility that photosynthetic eukalyotes inhabited the earth two biion years ago.
Sequence analysis to suggest that coronaviruses and toroviruses are related and that recombtition has played a role in their evolution.
Comparison
Volume 2
Number 1
1992
33