Combining data in phylogenetic analysis

Huelsenbeck, John P.; Bull, J. J.; Cunningham, Colleen

doi:10.1016/0169-5347(96)10006-9

Cited by 778 publications

(403 citation statements)

References 34 publications

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“…Repetitive minisatellite regions in the intron of EF in N. ribis were excluded. Congruence amongst all loci were confirmed using partition homogeneity tests (Farris et al, 1995;Huelsenbeck et al, 1996). PAUP (Phylogenetic Analysis Using Parsimony) version 4.0b10 (Swofford, 2003) was used to determine phylogenetic relationships for the single and combined data sets.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

Sakalidis

Hardy

Burgess

2011

Molecular Phylogenetics and Evolution

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Section: Phylogenetic Analysesmentioning

confidence: 99%

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

Sakalidis

Hardy

Burgess

2011

Molecular Phylogenetics and Evolution

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“…We investigated the degree of heterogeneity between the two gene fragments using the incongruence length differential (ILD) test of (Farris et al, 1994; see also Huelsenbeck et al, 1996;Whelan et al, 2001) as implemented in PAUP*, version 4.0b10 (Swofford, 2001) with settings as follows: 100 replicates, heuristic search using the tree bisection and reconnection (TBR) branch swapping algorithm. This test is used to determine whether significantly more evolutionary steps are required when data partitions are pooled rather than analyzed separately.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Testing alternative vicariance scenarios in Western Mediterranean discoglossid frogs

Fromhage

Vences

Veith

2004

Molecular Phylogenetics and Evolution

111

102

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Dated molecular phylogenies are often used to interpret evolutionary history with respect to paleogeographic events. Where more than one interpretation is possible, it is desirable but difficult to assess the alternatives in an objective manner. The present work demonstrates a formalized method for testing molecular clock calibrations and biogeographic scenarios based on them. We assessed the plausibility of several previously published biogeographic hypotheses, using the frog genera Alytes, Discoglossus, and Bombina as model groups. Our data set comprised ca. 900 bp of partial mitochondrial 16S and 12S rRNA gene sequences (both genes evolved in a clock-like manner across genera) from nearly all the species and subspecies in the three genera. We tested several calibrations of a molecular clock, which resulted in competing temporal settings for the evolution of taxa. Although only one scenario was in complete accordance with paleogeographic data, statistical testing did not reject the alternatives. Limitations encountered with the present approach may be overcome by more comprehensive analyses in future.

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“…ITS, EF1-α, and ACT sequence datasets were examined for congruence using the Partition Homogeneity Test in PAUP (Farris et al 1995;Huelsenbeck et al 1996). Selected isolates of Pallidocercospora heimii, Pseudocercospora norchiensis and Teratosphaeria aurantia, obtained from Eucalyptus (Pérez et al 2009b), were included as references to confirm genetic similarity.…”

Section: Dna Extraction Pcr Sequencing and Phylogenetic Analysismentioning

confidence: 99%

Species of Mycosphaerellaceae and Teratosphaeriaceae on native Myrtaceae in Uruguay: evidence of fungal host jumps

et al. 2013

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Mycosphaerella species are well-known causal agents of leaf diseases on many economically and ecologically important plant species. In Uruguay, a relatively large number of Mycosphaerellaceae and Teratosphaeriaceae are found on Eucalyptus, but nothing is known of these fungi on native Myrtaceae. The aim of this study was to identify Mycosphaerellaceae and Teratosphaeriaceae species associated with leaf diseases on native Myrtaceae in Uruguay and to consider whether host jumps by the pathogen from introduced Eucalyptus to native Myrtaceae have occurred.Several native forests throughout the country were surveyed with special attention given to those located close to Eucalyptus plantations. Five species belonging to the Mycosphaerellaceae and Teratosphaeriaceae clades were found on native Myrtaceous trees and three of these had previously been reported on Eucalyptus in Uruguay. Those occurring both on Eucalyptus and native Myrtaceae included Pallidocercospora heimii, Pseudocercospora norchiensis andTeratosphaeria aurantia. In addition, Mycosphaerella yunnanensis, a species known to occur on Eucalyptus but not previously recorded in Uruguay, was found on leaves of two native Myrtaceous hosts. Because most of these species occur on Eucalyptus in countries other than Uruguay, it appears that they were introduced in this country and have adapted to be able to infect native Myrtaceae. These apparent host jumps have the potential to result in serious disease problems and they should be carefully monitored.

show abstract

Combining data in phylogenetic analysis

Cited by 778 publications

References 34 publications

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum–Neofusicoccum ribis species complex

Testing alternative vicariance scenarios in Western Mediterranean discoglossid frogs

Species of Mycosphaerellaceae and Teratosphaeriaceae on native Myrtaceae in Uruguay: evidence of fungal host jumps

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