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W C Wheeler

Publications and source records attributed to W C Wheeler.

9 recordsLinked to original sources
PubMed1999

On gaps.

Gaps result from the alignment of sequences of unequal length during primary homology assessment. Viewed as character states originating from particular biological events (mutation), gaps contain historical information suitable for phylogenetic analysis. The effect of gaps as a source of phylogenetic data is explored via sensitivity analysis and character congruence among different data partitions. Example data sets are provided to show that gaps contain important phylogenetic information not recovered by those methods that omit gaps in their calculations. However, gap cost schemes are arbitrary (although they must be explicit) and thus data exploration is a necessity of molecular analyses, while character congruence is necessary as an external criterion for hypothesis decision.

Animals↗
PubMed1996

Molecular evolution and phylogenetic utility of the polyubiquitin locus in mammals and higher vertebrates.

The product of ubiquitin genes is a small protein involved in intracellular sorting of other proteins. The locus consists of tandemly arrayed, uninterrupted copies of the gene. As several studies have noted, the Polyubiquitin locus is a model system for studying concerted evolution. While the protein is among the most conserved known, individual copies within an organism show variation in nucleotide sequence despite clear evidence of concerted evolution. When treated as individuals, repeats from a given locus form a monophyletic group. Furthermore adjacent copies often cluster, suggestive of the mechanism of concerted evolution. Due to this concerted evolution of repeats (and loci in organisms with multiple polyubiquitins), sequencing of heterogeneous PCR products consisting of all the repeats in a given organism may yield phylogenetic signal, as with other multicopy genes. We test this possibility through 22 original sequences using primers designed so that only tandem copies are amplified. Using these and previously published data, we further explore these phenomena in higher vertebrates and mammals in particular. We suggest that multiple locus duplications have occurred within mammals. Positional codon bias is strongly evident. We also find substitutional bias with regard to codon type. GC content of the locus appears to be generally high across vertebrates. Intraorganismal variation is tallied as an indication of frequency of change in codon position and transition/transversion ratios to further elucidate the tempo and mode of molecular evolution. Using these data, a weighting scheme for ubiquitin is also presented. Despite the gene's high GC content, transitional changes still appear more frequent. While the phylogenetic utility of ubiquitin does not appear great, its mechanistic insights seem far from exhausted.

Amino Acid Sequence↗
PubMed1995

Elision: a method for accommodating multiple molecular sequence alignments with alignment-ambiguous sites.

The process of multiple sequence alignment provides homology statements for the phylogenetic analysis of molecular data. Unfortunately, multiple alignments are frequently nonunique. Two sources of these multiple alignments are analysis based on different sets of alignment parameter values (gap:change cost ratios) and nonunique equally costly alignments based on a single set of alignment parameters. By "eliding" these individual alignments into a single grand alignment, phylogeny that is weighted toward those positions that align more consistently can be reconstructed. Positions that show greater variation among alignments will be relatively downweighted. The technique results in a weighting procedure that is a posteriori and based on the evidence established from the original sequence alignments.

Alligators and Crocodiles↗
PubMed1994

Higher level relationships of the arctoid Carnivora based on sequence data and "total evidence".

The relationships of the lesser or red panda, Ailurus, have remained elusive even as any doubts about the identity of the giant panda as a bear have been erased. While usually classified as a member of the Procyonidae (raccoons), recent anatomical studies have suggested that the red panda may not fall in any of the arctoid carnivore families but instead may reflect an early offshoot of the lineage leading to ursids (bears) and pinnipeds (seals, sea lions, and walruses). Sequence data from the cytochrome b and 12S genes for multiple representatives of all relevant families support this hypothesis. Such a systematic position makes this threatened species particularly worthy of conservation. Sequence data alone, as well as a combined analysis of the sequence and anatomical data, strongly support a single origin of pinnipeds and their aquatic adaptations, lending some resolution to the general disagreement about familial relationships in this group. These molecular data also support canids as the basal members of this caniform clade, but are unresolved with respect to whether mustelids or procyonids constitute the sister group to the (ursid, pinniped, Ailurus) clade. There is support for the notion that skunks are a genetically divergent and possibly nonmustelid lineage.

Animals↗
PubMed1994

Sources of ambiguity in nucleic acid sequence alignment.

The discussion of molecular sequence alignment is becoming more prominent in studies of molecular systematics and evolution. As the basis for initial homology statements, alignment is crucial to comparative molecular biology. Although fundamental, alignment is not a process which necessarily yields objective, precise results. Ambiguities can appear in alignment due to a number of factors. Three such sources of ambiguity are discussed here. These are ambiguity in the establishment of alignment parameters, pair-wise order and individual "path" variation. The first arises from the necessary but empirically untestable assumptions of gap costs and other factors which are required to align sequences objectively. The second is due to the possible existence of non-unique solutions to the same alignment parameters in heuristic and exact solutions. The third is a result of multiple optimal paths within single alignments, potentially generating huge numbers of equally costly but unique alignments. Some of the problems with and several possible solutions to the difficult situation of non-unique alignments are discussed.

Algorithms↗
PubMed1993

Collection and storage of invertebrate samples.

The validity of any comparative study is dependent on the reliability of the identification of the samples in the study. Not all researchers are experts in the field of identification of samples, nor do all researchers have quick and ready access to expert systematists who can accomplish the task of identification. The importance of verification of sample identity for comparative studies is vital. We describe several methods by which researchers can obtain and identify samples from the wild, and we suggest methods by which voucher samples can be obtained for future reference to these collected samples. We outline alternatives to collection of samples from the wild, such as purchase from stock centers and biological supply companies. Museum collections can also be extremely helpful in obtaining complete organismal samples for comparative studies.

Academies and Institutes↗
PubMed1988

Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications.

Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of secondary structure are incongruent with those constructed on the basis of positions that are not. Furthermore, phylogeny reconstruction using these nonpairing bases is concordant with other, morphological data.

Animals↗