Computational protocol: Genetic and phenotypic characterization of a hybrid zone between polyandrous Northern and Wattled Jacanas in Western Panama

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Protocol publication

[…] We sequenced a 652 base pair fragment of the mitochondrial cytochrome oxidase I gene (COI: the DNA barcode fragment) [] from 59 Panamanian jacanas, as well as two specimens from eastern Honduras provided for our study by J. Klicka and the Marjorie Barrick Museum. We chose this gene to take advantage of existing sequence data on Genbank for jacanas from diverse geographic regions, which were also added to the dataset (N = 10). Laboratory procedures follow standard methods that have been described elsewhere []. We attempted but were unable to generate sequence data from toe pad extractions from the Smith and Emlen series of specimens.The COI data were used to estimate the genetic distinctiveness of the two jacana species and infer the time of speciation between J. spinosa and J. jacana, and to evaluate the degree to which geography limits gene flow in jacanas (i.e. isolation-by-distance). We generated median-joining network in PopART []. We used MEGA [] to calculate the average distance using the HKY model of molecular evolution in order to compare divergence in jacanas to many other avian species for which genetic distance has been calculated using the HKY model [].We tested for the effect of geographic distance on genetic differences (i.e., isolation by distance) via a Mantel test implemented in the program Alleles in Space [], which compares genetic and geographic distances among individuals rather than populations. For both J. spinosa and J. jacana mtDNA sequence sets, we correlated uncorrected pairwise sequence divergence with pairwise geographic distance for all possible pairs. Significance of the correlation was determined by comparing the observed correlation to random correlations based on 10,000 permutations.In order to complement the mtDNA-based analyses of genetic introgression across the jacana hybrid zone, we sequenced two autosomal introns (gapdh 11: [], and 10551: []) for STRIBC specimens collected across Panama. Based on a preliminary assessment of sequence variation from a few samples from each geographic endpoint (outside the hybrid zone) of our sampling design, we identified a single nucleotide polymorphism for each intron: gapdh 3- anti-sense position 136 (cytosine-thymine: C-T transition), and 10551 position 153 (adenine-guanine: A-G transition). Positions are relative to aligned sequences of each intron for the J. spinosa sample MJM8238 (Genbank accessions: gapdh: KM891734, 10551: KM891735). […]

Pipeline specifications

Software tools PopART, MEGA, AIS
Application Population genetic analysis
Organisms Jacana jacana, Jacana spinosa