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Table 2 Phylogenetic studies which use quantitative analytical methods

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

  1. Abbreviations: md missing data, Tc Trypanosoma cruzi