An automated phylogenetic key for classifying homeoboxes

Sarkar, Indra Neil; Thornton, Joseph W.; Planet, Paul J.; Figurski, David H.; Schierwater, Bernd; DeSalle, Rob

doi:10.1016/s1055-7903(02)00259-2

Cited by 106 publications

(99 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Placement of these morphologically classified specimens was used to identify the clades corresponding to each of the 3 taxonomic groups. Finally, following Kershaw et al (2013), we applied characteristic attributes (CAs) diagnosis (Davis & N ixon 1992, Sarkar et al 2002, Lowenstein et al 2009) to controlregion sequences of B. e. edeni, B. e. brydei, B. omurai, and the haplotypes from the GOMx whales. We first used the 9 diagnostic sites identified by Kershaw et al (2013) to try to classify the GOMx Bryde's whales to the recognized subspecies.…”

Section: Methodsmentioning

confidence: 99%

Genetic evidence reveals a unique lineage of Bryde’s whales in the northern Gulf of Mexico

Rosel¹,

Wilcox²

2014

Endang. Species. Res.

View full text Add to dashboard Cite

Bryde's whales Balaenoptera edeni are the only year-round resident baleen whale species in the northern Gulf of Mexico (GOMx). The current population abundance estimate is 33 (CV 1.07) and the population is severely restricted in range. We characterized genetic diversity and phylogenetic relationships of these whales to other members of the Bryde's whale complex. We analyzed DNA sequence data from 3 mitochondrial DNA (mtDNA) and 9 nuclear genes, and examined 42 nuclear microsatellite loci for 21 Bryde's whale samples collected in the GOMx and 2 from the western North Atlantic. mtDNA diversity was extremely low; only 2 haplotypes were found in the first 375 bp of the control region and no variability in cytb or cox1 genes was seen. Twenty-five microsatellite loci were monomorphic, 16 had 2 or 3 alleles, and 1 had 4 alleles. Most nuclear genes exhibited shared alleles across balaenopterid species. Phylogenetic reconstruction using the control region and all published Bryde's whale sequences revealed that GOMx Bryde's whale haplotypes are evolutionarily distinct from other members of the Bryde's whale complex examined to date. Within the first 375 bp of the control region, we found 25−26 fixed differences between GOMx haplotypes and those from sei whales and the 2 recognized Bryde's whale subspecies. The GOMx whales are as divergent as these subspecies and species are from each other. The level of divergence suggests a unique evolutionary trajectory worthy of its own taxonomic standing. The small population size and markedly low genetic diversity raise conservation concern for this unique group of whales. KEY WORDS: Bryde's whale complex · Balaenoptera edeni · Mitochondrial DNA · Control region · CetaceanResale or republication not permitted without written consent of the publisher

show abstract

Section: Methodsmentioning

confidence: 99%

Genetic evidence reveals a unique lineage of Bryde’s whales in the northern Gulf of Mexico

Rosel¹,

Wilcox²

2014

Endang. Species. Res.

View full text Add to dashboard Cite

show abstract

“…Based on peptide sequence identity with known Hox genes, DNA sequences could be assigned unambiguously to paralog groups (PG) 1, 3, 9, 11, 13, as well as to a more poorly resolved ''middle group'' gene (paralog groups 4-7). The automated phylogenetic key for classifying homeoboxes described by Sarkar et al (2002) unfortunately is not applicable since it requires homeobox fragments that are longer than 27 amino acids.…”

Section: Methodsmentioning

confidence: 99%

PCR survey of hox genes in the goldfish Carassius auratus auratus

Luo

Stadler

et al. 2006

J Exp Zool Pt B

View full text Add to dashboard Cite

A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event.

show abstract

“…C. The DNA sequence attributes in the two columns by themselves constitute two private DNA positions. However, in combination these two columns provide a 'pure' diagnostic combination (AA versus AG or GA; 'compound pure' character in the terminology of Sarkar et al 2002). D. The four columns marked by the shading for D are neither diagnostic nor private.…”

Section: A Character Based Barcoder Proposedmentioning

confidence: 99%

“…From these advantages it could be argued that a corroborated total evidence tree could be used as a guide tree for identifying the phylogenetic affinities of an unknown individual's sequence, assuming that the query sequence is one of the gene regions used to construct the total evidence tree. There are bioinformatics tools to aid in the placement of a query sequence based on the presence of shared characters that are diagnostic for nodes on the tree (Sarkar et al 2002). However, there is a third drawback to the use of a tree building approach to species identification.…”

Section: Introduction: Building a Better Dna Barcodermentioning

confidence: 99%

The unholy trinity: taxonomy, species delimitation and DNA barcoding

DeSalle

Egan

Siddall

2005

Phil. Trans. R. Soc. B

Self Cite

835

749

View full text Add to dashboard Cite

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings-Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.

show abstract

An automated phylogenetic key for classifying homeoboxes

Cited by 106 publications

References 21 publications

Genetic evidence reveals a unique lineage of Bryde’s whales in the northern Gulf of Mexico

Genetic evidence reveals a unique lineage of Bryde’s whales in the northern Gulf of Mexico

PCR survey of hox genes in the goldfish Carassius auratus auratus

The unholy trinity: taxonomy, species delimitation and DNA barcoding

Contact Info

Product

Resources

About