Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)

Azevedo, Guilherme H.F.; Hedin, Marshal; Maddison, Wayne P.

doi:10.1016/j.ympev.2024.108109

Molecular Phylogenetics and Evolution

2024

DOI: 10.1016/j.ympev.2024.108109

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Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)

Guilherme H.F. Azevedo,

Marshal Hedin,

Wayne P. Maddison

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2024

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Cited by 1 publication

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PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites

Maddison

2024

PeerJ

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In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees.

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PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites

Maddison

2024

PeerJ

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Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae)

Cited by 1 publication

References 80 publications

PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites

PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites

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