Computational protocol: Spatial, environmental and anthropogenic effects on the taxon composition of hybridizing Daphnia

Similar protocols

Protocol publication

[…] All the individuals were assayed at four polymorphic allozyme loci (AAT, AO, PGI, PGM) using cellulose acetate electrophoresis (see ). These loci were used to identify hybrid classes with NewHybrids () that uses Bayesian statistics to calculate a posterior probability that reflects the level of certainty of an individual belonging to a specific hybrid category. Probability threshold for allocation was set to 95% or more; the remaining individuals could not be attributed with confidence to a specific hybrid class (Fx) and therefore were excluded from subsequent statistical analyses. Since NewHybrids can only assign individuals to two hybridizing taxa, each lake population was divided into taxa pairs based on AAT and AO loci that are diagnostic for D. galeata, D. hyalina and D. cucullata (; ). Individuals incorporating alleles from all three parental taxa (Fxhgc) were excluded from the analysis with NewHybrids. In this way, we discriminated between D. galeata (Pgal), D. hyalina (Phyl), D. cucullata (Pcuc), D. galeata×D. hyalina F1-hybrids (F1hg), D. hyalina×D. cucullata F1-hybrids (F1hc), and D. galeata×D. hyalina×D. cucullata Fx-hybrids (Fxhgc). [...] Environmental parameters were log-transformed if needed. Since the Daphnia taxon dataset contains many zeros, we chose canonical correspondence analysis (CCA), a multivariate technique that considers only proportional relationships between variables and removes all differences between any data formats (see ). The CCAs as well as follow-up statistical tests (e.g. classical variation partitioning) were performed with the Canoco package, v. 4.5 (). Variation partitioning with adjustments was performed using the program of . Discriminant function analysis (DFA) and subsequent testing of selected variables with a Mann–Whitney U-test were performed with Statistica for Windows, release v. 7.1 (StatSoft, Inc.). Details of analyses are given below. […]

Pipeline specifications

Software tools NewHybrids, Statistica
Applications Miscellaneous, Population genetic analysis
Organisms Homo sapiens
Chemicals Phosphorus