Computational protocol: Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

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Protocol publication

[…] We analysed a total of 99 new wild isolates of C. briggsae (53 from French Guiana, 46 from other world-wide localities). Note that four French Guiana isolates (NIC88, NIC106, NIC107, NIC108) were analysed in Jovelin & Cutter []. Based on a set of six nuclear loci used previously [,,,], we investigated the relationships of the 57 new isolates for which data were collected for all six loci, relative to a collection of 132 isolates that were used in previous studies on C. briggsae diversity [,,,]. We also obtained sequence data for up to five of these loci for the remaining new isolates, which informed some analyses (Additional file ). Multiple sequence alignments were constructed for each locus in BioEdit [] and manually edited for indel polymorphisms. We inferred the relationships among isolates with concatenated sequences from the set of six loci using unrooted neighbour-networks generated with a Jukes-Cantor distance in the program SplitsTree 4.10 []. Neighbour-networks are useful for representing the relationships among individuals of the same species for which recombination events may be non-negligible []. We then measured differentiation and divergence between phylogeographic groups using FST[] and Dxy, the average number of nucleotide substitutions per site between groups []. We also measured nucleotide polymorphism [] at each locus taken separately using DnaSP v.5 [] and took the average across loci in order to investigate nucleotide diversity at multiple spatial scales in C. briggsae. […]

Pipeline specifications

Software tools BioEdit, SplitsTree, DnaSP
Application Phylogenetics
Organisms Caenorhabditis elegans, Homo sapiens, Caenorhabditis briggsae
Diseases Nematode Infections, Pulmonary Fibrosis