From: Geographical, landscape and host associations of Trypanosoma cruzi DTUs and lineages
Article | Hypothesis/Aim | Parasite population | Sample size | Geographical scale | Temporal scale (yrs) | Population genetic analysis | Outgroup | Statistical analytical method |
---|---|---|---|---|---|---|---|---|
Flores-Lopez & Machado [18] | Reconstruction of the evolutionary history of Tc | Isolates | 7 | Tc stocks | md | Nucleotide sequences from 32 loci | T. c. marinkellei, T. vespertilionis | Test of selection, divergence time estimates |
Venegas et al. [27] | Specific host-parasite association in Chilean populations of Tc | Original | 117 | Chile | 2 | Microsatellite loci | none | Phylogram tree (NJ)/Genetic differentiation |
Barnabe et al. [114] | Subsample analyses of MLMT structuring among reference stocks belonging to known DTUs | Isolates | 94 | Bolivia and Peru | 32 | Microsatellite loci | none | NJ trees/Fixation indices FIS and FST/Genetic diversity Hs/ANOVA |
Freitas et al. [88] | Dissect the multilocus genotypes into their constituent haploid genome blocks to understand Tc evolutionary history | Isolates | 75 | Brazil | md | Microsatellite loci, 24SrRNA, cox2 sequencing/ RFLP | none | Distance matrices, multidimensional scaling and NJ tree/Haplotype inference and network construction |
Ienne et al. [89] | Test hybridization hypothesis | Isolates | 9 | Tc stocks | md | 195 SAT | none | Phylogenetic inference (NJ)/Network |
Lauthier et al. [127] | Stability of multilocus genotypes as the required condition for any molecular epidemiology approach (strain typing) | Isolates | 32 | Argentina | md | Multilocus sequence typing (10 targets) | T. c. marinkellei | Phylogenetic tree/Genotype network |
Lewis et al. [90] | Origins and evolution of Tc at several overlapping levels | Isolates | 35 | South America | md | GPI, cox2-nad1, microsatellite loci | none | Bayesian Inference, microsatellite analysis |
Llewellyn et al. [91] | Within-host diversity in TcI | Isolates | 211 | Bolivia, Venezuela and Brazil | 5 | Microsatellite loci | none | Genetic distance (DAS), FIS (FSTAT), AMOVA and index of association |
Macedo et al. [92] | Usefulness of microsatellite typing in population genetic studies of Tc | Isolates | 53 | Tc stocks | md | Microsatellite loci | none | Wagner network |
Oliveira et al. [115] | Population structure of the parasite | Isolates | 30 | Brazil and Colombia | md | 8 microsatellites | none | Wagner network |
Oliveira et al. [93] | Population structure of Tc | Isolates | 54 | md | md | 8 microsatellites | none | Tests for Hardy-Weinberg and linkage disequilibrium/Wagner network |
Pena et al. [94] | Population structure of TcI | Isolates | 75 | Tc stocks | md | Microsatellite and mitochondrial sequences | none | NJ/ Network |
Ramirez et al. [116] | Genetic variability within TcI clones and concordance with the established genotypes | Isolates | 70 | Colombia | md | cytb sequencing | T. c. marinkellei | Phylogenetic tree/Genotype network |
Ramirez et al. [128] | Contemporary cryptic sexuality in Tc | Isolates | 369 | Colombia | 10 | Microsatellite and mitochondrial sequences | DTUII and DTUIV | Genetic diversity/NJ/ML/BEAST |
Ramirez et al. [117] | Nuclear MLST markers to unravel the genetic structure of TcI in Colombia | Isolates | 50 | Colombia | 11 | Nuclear multilocus sequence typing | DTUII and DTUIV | Genetic diversity and diploid sequence types (DSTs) |
Telleria et al. [95] | Association between Tc subspecific phylogenetic diversity and levels of protein expression | Isolates | 26 | Tc stocks | md | Proteomics data | T. c. marinkellei | MLEE genetic distances and proteomic Euclidian distances |
Tomazi et al. [96] | Hybrids are of polyphyletic origin, evolving independently from various hybridization events | Isolates | 26 | South America | md | Sequences of SSU rDNA, EF-1α, actin, DHFR-TS and TR genes | none | Phylogeny inference and network geneologies |