carpophilus: Sequence alignments of _Carpophilus_ species

Description Usage Format Source Examples

Description

DNA

Usage

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Format

Objects of class ‘DNAbin’, stored as matrices.

carpoCOI is an alignment of 105 sequences from the 5' end of cytochrome c oxidase subunit 1, and are 576 bp in length. Sequences are available on Genbank as accession numbers GU217433 through GU217530.

carpo28S is an alignment of 43 sequences from the 5' end of the D1-D2 region of the 28S ribosomal RNA gene, and are 734 bp in length. Sequences are available on Genbank as accession numbers GU217391 through GU217432.

carpoITS is an alignment of 53 sequences from the internal transcribed spacer 2 (ITS2) region in the nuclear ribosomal encoding cistrons, and are 504 bp in length. Sequences are available on Genbank as accession numbers GU217338 through GU217390.

Sequences are named in the following format: "accessionNumber|speciesCode|geographicCode".

Species codes are made up of three blocks of four characters each. The first block encodes the genus, the second the species, and the third the subspecies.

Geographic codes are as follows: AUS–Australia, BIS–Bismarck Islands, FIJ–Fiji, HAW–Hawaii, KER–Kermadec Islands, NAU–Nauru, NCL–New Caledonia, NZL–New Zealand, SAM–Samoa, SOC–Society Islands (French Polynesia), TON–Tonga, TUB–Austral (Tubuai) Islands (French Polynesia), TUV–Rotuma Island (close to Tuvalu), USA–United States of America, VAN–Vanuatu

Source

Brown, S. D. J., Armstrong, K. F., and Cruickshank, R. H. (2012). Molecular phylogenetics of a South Pacific sap beetle species complex (_Carpophilus_ spp., Coleoptera: Nitidulidae). _Molecular Phylogenetics and Evolution_ *64(3)* 428-440. URL: http://dx.doi.org/10.1016/j.ympev.2012.04.018

Examples

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data(carpophilus)

#subspecies vectors
carpoCOIsspp <- sapply(strsplit(dimnames(carpoCOI)[[1]], split = "\\|"), function(xx) xx[2])
carpo28Ssspp <- sapply(strsplit(dimnames(carpo28S)[[1]], split = "\\|"), function(xx) xx[2])
carpoITSsspp <- sapply(strsplit(dimnames(carpoITS)[[1]], split = "\\|"), function(xx) xx[2])

#species vectors
carpoCOIspp <- substr(carpoCOIsspp, 1,  8)
carpo28Sspp <- substr(carpo28Ssspp, 1,  8)
carpoITSspp <- substr(carpoITSsspp, 1,  8)

spiderDev documentation built on May 2, 2019, 5:23 p.m.