Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study

Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

“…Portions of the nuclear genes Ptr (si:ch211-105n9.1), hypothetical protein LOC564097 (PTR), ectodermal-neural cortex 1-like protein (ENC1), similar to SH3 and PX domain containing 3 gene (SH3PX3) and early growth response protein (EGR) were amplified and sequenced with previously described primers (Chen et al, 2008;Li et al, 2007). Sequence-specific amplifications were performed by PCR in a final 50 ll volume containing 5 ll of 10Â buffer (Takara), 5 mM dNTP, 1.5U Taq polymerase (Takara), and 1 lM of oligonucleotide primers, and 1 lg DNA.…”

“…Sequence-specific amplifications were performed by PCR in a final 50 ll volume containing 5 ll of 10Â buffer (Takara), 5 mM dNTP, 1.5U Taq polymerase (Takara), and 1 lM of oligonucleotide primers, and 1 lg DNA. Thermocycling conditions were consistent with the previous studies (Chen et al, 2008;Li et al, 2007). The result was visualized on low-melting agarose gels and sequencing was performed on ABI3730xl sequencer (Applied Biosystems, Foster City, CA, USA).…”

“…One of the questions we ask herein is can the enhanced methods of data partitioning improve our ability to resolve the phylogenetic relationships of these problematic groups at both the apical and basal levels. Resolution of the phylogenetic placement of the genus Tinca has been problematic using all types of data, either morphological or molecular (Chen et al, 2008;Chen, 1984;Gilles et al, 1998;Howes, 1991;Zardoya and Doadrio, 1999). Cavender and Coburn concluded from the morphological matrix of Chen that Tinca was more closely allied to the subfamily Cyprininae.…”

“…Rather than employing standard genes that have previously used in many other studies on Cypriniformes or Cyprinidae, we intentionally used nuclear markers that have been used successfully for elucidating the relationships of teleost clades (Chen et al, 2008;Li et al, 2007). Analysis of these genes yielded remarkably new findings not only in the resolution of formally difficult clades and species but also critical insights into the importance of not shortcutting phylogenetic analyses to simple single matrix or gene model estimation but a full-scale estimation of individual base pairs.…”

“…A few multi-gene phylogenetic analyses are available for Cyprinidae and these are only available for some endemic taxa in North America (Chen and Mayden, 2009;Chen et al, 2008). Limited taxon and gene sampling, as well as stochastic error at a limited number of parsimony informative sites and random noise, constitute major limitations of standard phylogenetic analyses.…”