A novel primer set for multilocus phylogenetic inference in East African cichlid fishes.

Meyer, Britta and Salzburger, Walter (2012) A novel primer set for multilocus phylogenetic inference in East African cichlid fishes. Molecular Ecology Resources, 12 (6). pp. 1097-1104. DOI 10.1111/j.1755-0998.2012.03169.x.

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Supplementary data:

Abstract

The cichlid fishes in the East African Great Lakes are a prime model system for the study of adaptive radiation. Therefore, the availability of an elaborate phylogenetic framework is an important prerequisite. Previous phylogenetic hypotheses on East African cichlids are mainly based on mitochondrial and/or fragment-based markers, and, to date, no taxon-rich phylogeny exists that is based on multilocus DNA sequence data. Here, we present the design of an extensive new primer set (24 nuclear makers) for East African cichlids that will be used for multilocus phylogenetic analyses in the future. The primers are designed to work for both Sanger sequencing and next-generation sequencing with the 454 technology. As a proof of principle, we validate these primers in a phylogenetically representative set of 16 cichlid species from Lake Tanganyika and main river systems in the area and provide a basic evaluation of the markers with respect to marker length and diversity indices

Document Type: Article
Additional Information: Table S1 List of the 24 genes used for primerdesign. Information is provided with regard to the alignment lengthused for primer design; the percentage of variable andparsimony-informative sites without the outgroup; the number ofpolymorphic sites (SNPs), the location in the different species andits percentage including the outgroup; average p-distancecalculated with complete deletion and without the outgroup; itsrange and SE calculated with 500 bootstrap replicates; and averagep-distance including only base pairs from exon or intron withoutthe outgroup; the recommended model from JMODELTEST 0.1.1 on the basis of the Bayesian information criterion (BIC) with its computed likelihood scores; the GO terms from annotated fish sequences from UniProtKB (The UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Table S2 List of the 24 genes used for primerdesign. Information about the number of successful PCR andsequencing reactions; further used sequences and their Accessionnumber of GenBank or other source; the percentage of missing data(due to sequencing errors); used annealing temperature in the PCRand used Taq polymerase; +/+ designates successful PCR andsequencing reaction, −/− both unsuccessful, +/− PCR successful and sequencing unsuccessful; indicating possible reason for failed sequencing reaction. Table S3 List of used species, 24 markers and GenBank Accession numbers (asterisks indicate the usage of other unpublished primer pairs) http://www.ncbi.nlm.nih.gov/genbank/.
Keywords: adaptive radiation; cichlid species flocks; nuclear markers; organismal diversification
Refereed: Yes
Open Access Journal?: No
Publisher: Wiley
Date Deposited: 02 Jul 2014 12:48
Last Modified: 09 Nov 2018 13:13
URI: https://oceanrep.geomar.de/id/eprint/25079

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