Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies

Kumar, Sudhir; Gadagkar, Sudhindra R.

doi:10.1007/s002390010118

Cited by 95 publications

(61 citation statements)

References 28 publications

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“…In total, 249 sequences of BenA (for 64 species) and 282 sequences of ITS (for 49 species) were downloaded, aligned by using ClustalW with BioEdit (38), and analyzed in MEGA3 (39). For all analyses, nucleotide-sequence divergences and dendrograms were calculated with the neighborjoining algorithm and the Kimura two-parameter model; the performance of this method is comparable with other techniques when distances are low (40) and large species assemblages are analyzed (41).…”

Section: Methodsmentioning

confidence: 99%

Prospects for fungus identification usingCO1DNA barcodes, withPenicilliumas a test case

Seifert

Samson

deWaard

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

328

266

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DNA barcoding systems employ a short, standardized gene region to identify species. A 648-bp segment of mitochondrial cytochrome c oxidase 1 (CO1) is the core barcode region for animals, but its utility has not been tested in fungi. This study began with an examination of patterns of sequence divergences in this gene region for 38 fungal taxa with full CO1 sequences. Because these results suggested that CO1 could be effective in species recognition, we designed primers for a 545-bp fragment of CO1 and generated sequences for multiple strains from 58 species of Penicillium subgenus Penicillium and 12 allied species. Despite the frequent literature reports of introns in fungal mitochondrial genomes, we detected introns in only 2 of 370 Penicillium strains. Representatives from 38 of 58 species formed cohesive assemblages with distinct CO1 sequences, and all cases of sequence sharing involved known species complexes. CO1 sequence divergences averaged 0.06% within species, less than for internal transcribed spacer nrDNA or ␤-tubulin sequences (BenA). CO1 divergences between species averaged 5.6%, comparable to internal transcribed spacer, but less than values for BenA (14.4%). Although the latter gene delivered higher taxonomic resolution, the amplification and alignment of CO1 was simpler. The development of a barcoding system for fungi that shares a common gene target with other kingdoms would be a significant advance.␤-tubulin ͉ cytochrome c oxidase I ͉ DNA barcoding ͉ internal transcribed spacer ͉ species identification

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Section: Methodsmentioning

confidence: 99%

Prospects for fungus identification usingCO1DNA barcodes, withPenicilliumas a test case

Seifert

Samson

deWaard

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

328

266

View full text Add to dashboard Cite

show abstract

“…The NJ methodology is the standard method of phylogenetic inference in DNA barcoding studies (Hebert et al, 2003); its use in DNA barcoding studies is in part due to its strong track record in being able to rapidly analyze large species assemblages (Kumar and Gadagkar, 2000). The chosen molecular substitution model was the computationally simple Kimura-two-parameter (K2P) (Kimura, 1980) which is the standard model of molecular evolution used in DNA barcoding studies (Hebert et al, 2003).…”

Section: Phylogenetic Analyses and Hypotheses Testingmentioning

confidence: 99%

A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes)

et al. 2008

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DNA barcoding is a recently proposed global standard in taxonomy based on DNA sequences. The two main goals of DNA barcoding methodology are assignment of specimens to a species and discovery of new species. There are two main underlying assumptions: i) reciprocal monophyly of species, and ii) intraspecific divergence is always less than interspecific divergence. Here we present a phylogenetic analysis of the family Potamotrygonidae based on mitochondrial cytochrome c oxidase I gene, sampling 10 out of the 18 to 20 valid species including two non-described species. Potamotrygonidae systematics is still not fully resolved with several still-to-be-described species while some other species are difficult to delimit due to overlap in morphological characters and because of sharing a complex color patterns. Our results suggest that the family passed through a process of rapid speciation and that the species Potamotrygon motoro, P. scobina, and P. orbignyi share haplotypes extensively. Our results suggest that systems of identification of specimens based on DNA sequences, together with morphological and/or ecological characters, can aid taxonomic studies, but delimitation of new species based on threshold values of genetic distances are overly simplistic and misleading.

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“…We used a short fragment (221 bp) of dsrA to reconstruct phylogenetic trees. Sequence length has a profound effect on reliable reconstruction of phylogenetic trees (Kumar & Gadagkar 2000). Pérez-Jiménez et al (2001) tested whether the length of dsrAB used for the analysis had a significant effect on the tree topology by reconstructing phylogenetic trees for alignments of different length dsrAB sequences and found that the general topology of all trees was consistent with the previous dsrAB tree based on fulllength dsrAB fragments (Minz et al 1999, Wagner et al 1998.…”

mentioning

confidence: 94%

Abundance and diversity of sulphate-reducing bacterioplankton in Lake Suigetsu, a meromictic lake in Fukui, Japan

Kondo¹,

Osawa²,

Mochizuki³

et al. 2006

Plankton Benthos Res

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Abstract:The depth distribution of sulphate-reducing bacteria (SRB) in the water column of a meromictic lake, Lake Suigetsu, Fukui, Japan was investigated using quantitative competitive PCR targeting the gene coding for portions of the a-subunit of dissimilatory sulphite reductase (dsrA). The total bacterial cell density (DAPI count) was 5Ϫ13ϫ10 6 cells mL Ϫ1 in the water column of the lake with maximum abundance occurring at the oxic-anoxic interface layer. SRBwere not detected in oxic surface water using competitive PCR. SRB were found in the anoxic waters below the oxycline ranging from 10 4 to 10 5 cells mL Ϫ1 , accounting for 0.3-8.9% of the total bacteria. The SRB cell densities were higher than previously estimated using the most-probable-number (MPN) method. Sequencing of the cloned PCR product of dsrA showed the existence of different SRB groups in the anoxic water. The majority of the dsrA sequences were associated with the Desulfosarcina-Desulfococcus-Desulfonema group and members of the Desulfobulbaceae family.Other dsrA clones belonged to the Desulfomicrobium and Desulfovibrio species as well as to a deeply branched group in the dsrA tree with no representatives from previously isolated SRB groups. These SRB species appear to be important for the sulphur and carbon cycle in the anoxic waters of Lake Suigetsu.

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Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies

Cited by 95 publications

References 28 publications

Prospects for fungus identification usingCO1DNA barcodes, withPenicilliumas a test case

Prospects for fungus identification usingCO1DNA barcodes, withPenicilliumas a test case

A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes)

Abundance and diversity of sulphate-reducing bacterioplankton in Lake Suigetsu, a meromictic lake in Fukui, Japan

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