Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

On gaps.

G Giribet1, W C Wheeler

  • 1Department of Invertebrates, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA.

Molecular Phylogenetics and Evolution
|October 6, 1999
PubMed
Summary
This summary is machine-generated.

Gaps in sequence alignments provide valuable phylogenetic data. Analyzing these gaps is crucial for accurate evolutionary relationship reconstruction, as omitting them leads to lost evolutionary information.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A combined approach to the phylogeny of Cephalopoda (Mollusca).

Cladistics : the international journal of the Willi Hennig Society·2021
Same author

Predicting the Impact of Describing New Species on Phylogenetic Patterns.

Integrative organismal biology (Oxford, England)·2021
Same author

A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages.

Molecular ecology resources·2013
Same author

Phylogeographical history of the sponge Crambe crambe (Porifera, Poecilosclerida): range expansion and recent invasion of the Macaronesian islands from the Mediterranean Sea.

Molecular ecology·2003
Same author

Exploring the behavior of POY, a program for direct optimization of molecular data.

Cladistics : the international journal of the Willi Hennig Society·2002
Same author

Efficiency of parallel direct optimization.

Cladistics : the international journal of the Willi Hennig Society·2002
Same journal

Pangenome analysis of Nocardia brasiliensis reveals phylogenetic divergence, high genomic diversity and widespread distribution of biosynthetic gene clusters involved in secondary metabolite biosynthesis.

Molecular phylogenetics and evolution·2026
Same journal

Adaptive introgression facilitates tropical plant evolution: Pandanus as a case study.

Molecular phylogenetics and evolution·2026
Same journal

Molecular phylogenetics of Andean killifish genus Orestias (Cyprinodontiformes: Orestiidae) with emphasis on the O. agassii species complex, a widespread Andean clade.

Molecular phylogenetics and evolution·2026
Same journal

Resolving fuzzy species limits: nuclear evidence for speciation by hybridisation in Amazonian Trichomanes ferns.

Molecular phylogenetics and evolution·2026
Same journal

Phylogenomic assessment of microhylid frogs reveals widespread taxonomic confusion in the Asterophryinae and establishes the timing of diversification in Australia.

Molecular phylogenetics and evolution·2026
Same journal

Phylogenomics, introgression, and demographic history of extant flamingos (Aves: Phoenicopteridae).

Molecular phylogenetics and evolution·2026
See all related articles

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Sequence alignment is fundamental to homology assessment.
  • Gaps arise from unequal sequence lengths and represent biological events like mutations.
  • Traditional methods sometimes exclude gaps, potentially losing phylogenetic information.

Purpose of the Study:

  • To investigate the phylogenetic significance of gaps in sequence data.
  • To demonstrate the utility of gaps as a source of evolutionary information.
  • To highlight the necessity of including gap data in phylogenetic analyses.

Main Methods:

  • Sensitivity analysis of gap data.
  • Character congruence assessment across different data partitions.
  • Utilizing example datasets to evaluate gap inclusion.

Related Experiment Videos

Main Results:

  • Gaps contain significant phylogenetic information often missed by gap-omitting methods.
  • The inclusion of gap data can alter or improve phylogenetic hypotheses.
  • Arbitrary gap cost schemes necessitate explicit data exploration.

Conclusions:

  • Gaps are a vital source of phylogenetic data that should be incorporated into analyses.
  • Character congruence serves as an essential external criterion for validating phylogenetic hypotheses derived from gap data.
  • Molecular data analyses require careful exploration, especially concerning gap interpretation.