Link to Additional File 4 (Matthew Parks, 03 January 2013)
Due to difficulties with the link to Additional File 4 (the Pinus plastome phylogeny), we have posted this file at the following URL where it may be accessed and downloaded:
Richard Cronn read full comment
Comment on: Parks et al. BMC Evolutionary Biology, 12:100
Incorrectness Table 2 Saatzucht Dr. Hege GbR (Veronique Troch, 11 December 2012)
The breeding company of triticale cultivars Partout and Amarillo mentioned in table 2 is Saatzucht Dr. Hege GbR, instead of Nordsaat Saatzucht GmbH. We apologize for this incorrectness. read full comment
Comment on: Troch et al. BMC Evolutionary Biology, 12:76
additional file missing? (Alejandra Vázquez-Lobo, 14 November 2012)
I was so curious about the phylogeny, although it seems like additional files 4 and 5 are the same, and I didn't find a tree. read full comment
Comment on: Parks et al. BMC Evolutionary Biology, 12:100
The origin of viruses (Steven Pelech, 25 September 2012)
The existence of giant viruses has been known for a while now, including the fact that they can sport genomes that feature over 1 million base pairs and encode over a thousand proteins, as exemplified with the Megavirus chiliensis. Most of the largest viruses target unicellular organisms such as protozoa and algae. By contrast, some of the smallest bacteria have ten-fold smaller genomes with 5-fold less encoded proteins than these giant viruses. Consequently, it is not hard to envision that all viruses originally evolved from invasive prokaryotes that eventually become mobile parasites that utilized the proteins encoded by their hosts to facilitate their own replication. The giant viruses discovered to date probably represent more recent transitions of parasitic prokaryotes into viruses.... read full comment
Comment on: Nasir et al. BMC Evolutionary Biology, 12:156
Technical Comment on ¿Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses¿ (Zsuzsanna Guba, 12 September 2012)
Technical Comment on ¿Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA... read full comment
Comment on: Magyari et al. BMC Evolutionary Biology, 11:66
Interesting result but details of program AlienG are needed for evaluation (PAul Lehmann, 28 June 2012)
The findings are interesting but are hard to evaluate thoroughly when they appear to be dependent on using an analytical program "AlienG" that seems to be undescribed. read full comment
Comment on: Ni et al. BMC Evolutionary Biology, 12:83
Regarding the screening of Heliconius for endosymbionts (Jeremy Kipling, 30 May 2012)
The authors state in the discussion that "this is the first published study in which the presence of endosymbionts is tested in Heliconius" and in the abstract that these were "the first tests for the presence of endosymbiontic [sic] bacteria in Heliconius." I wanted to correct this by referring to the 1995 paper by Werren, Windsor, and Guo here in which they screened three H. erato and one H. melpomene (see Table 2). Obviously a very small sample size, but still worth mentioning. read full comment
Comment on: Muñoz et al. BMC Evolutionary Biology, 11:358
Additional Genbank IDs (Ana Caicedo, 17 November 2011)
The list of Genbank IDs in the paper is incomplete. The following Genbank IDs also form part of this study:
JN808321-JN808432 read full comment
Comment on: Reagon et al. BMC Evolutionary Biology, 10:180
Reference 7 (Philippa Harris, 07 November 2011)
The full citation details of reference 7 are as follows:
Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
Soowon Cho et al. Syst Biol (2011) 60 (6): 782-796. doi: 10.1093/sysbio/syr079 read full comment
Comment on: Kawahara et al. BMC Evolutionary Biology, 11:182
Resolving differences with Fromhage & Kokko model. (Peter Nonacs, 19 August 2011)
Recently Fromhage and Kokko (FK: 2011, Nature Communications 2:397) modeled the same issue as the Nonacs (N) paper. The two papers differ with FK finding cooperation becomes more likely with monogamy and haplodiploidy, which is the opposite to the outcomes reported here. Nevertheless, there are several similarities across the two papers. Helping evolves only if the cost of allelic ‘free-riders’ can be overcome. As shown in both papers, alleles for helping behavior are at higher frequencies in helpers than in those being helped with certain mating combinations. This assortment cost creates within-group selection favoring non-helping alleles. Monogamy and haplodiploidy minimize such costs, hence producing the FK outcomes. In the N outcomes, this assortment cost creates... read full comment
Comment on: Nonacs BMC Evolutionary Biology, 11:58
Minor typographical errors (CAROLINA ISABEL MIñO, 19 August 2011)
Dear reader, we would like to communicate that, unfurtunately and in spite of the several revision stages, minor typographical errors were discovered in the final version of our manuscript published by BMC Evolutionary Biology. We sincerely hope that readers forgive us for these minor errors that do not undermine the quality of our publication. We deeply thank the BMC Editorial Team for extensive help when preparing our manuscript for publication. We assume full responsibility for the small typographical errors in the final version of our paper.
Readers can find below a detailed explanation of the errors in the publication:
• Page 9, line 11 of third paragraph on the left column: it should read Bubulcus ibis;
• Page 5, Figure 2 legend: it should read “Flow-... read full comment
Comment on: Miño et al. BMC Evolutionary Biology, 11:196
Errata (Bettina (Eveline) Schirrmeister, 04 July 2011)
Sentence 1: "A total of 2,065 16S rRNA gene sequences from the phylum cyanobacteria were downloaded from GenBank.", is not correct.
Instead it should read:
"A total of 2,064 16S rRNA gene sequences from the phylum cyanobacteria were downloaded from GenBank."
Phylogenetic analyses of all identified cyanobacteria
Sentence 4: "From the remaining 1,254 sequences (1235 characters) a phylogenetic tree was reconstructed running 10 maximum likelihood analyses as implemented in RAxML v7.0.4 .", is not correct.
Instead it should read:
"From the remaining 1,220 sequences (1261 characters) a phylogenetic tree was... read full comment
Comment on: Schirrmeister et al. BMC Evolutionary Biology, 11:45
Correction (Ovidiu Paun, 08 June 2011)
The distribution of Dactylorhiza traunsteineri from Figure 1 should include Ireland, in addition to Britain, Scandinavia and the Alps. read full comment
Comment on: Paun et al. BMC Evolutionary Biology, 11:113
Probing analysis presents a problem (Brig Klyce, 31 May 2011)
I congratulate Kim and Caetano-Anollés for a very probing analysis. But I think the conclusion presents a problem. A precellular "urancestor with functional complexity similar to that of extant life" is very hard to understand within darwinism. I expand upon this point slightly in an entry, "...more functional protein domains than the first cells!," and suggest another explanation on my blog about panspermia. read full comment
Comment on: Kim et al. BMC Evolutionary Biology, 11:140
Comparison with the nucleotide polymorphism in the entire gene sequence or the non-coding region (Sibin Yu, 29 March 2011)
In the Discussion section, the level of nucleotide polymorphism (pi = 0.00006) is for the non-coding region of OsAMT1;1 in O. sativa. Please note it is better to use the level of nucleotide polymorphism (pi = 0.00004) in the entire gene sequence for the comparison with that of the 111 chosen gene fragments, although both the levels lead to the same conclusion. read full comment
Comment on: Ding et al. BMC Evolutionary Biology, 11:61
Corrigendum (Pierre-Arthur Moreau, 28 February 2011)
A mistake has been detected after submission in Additional file 2: the cell J180 is filled "Submitted" and should be empty (no sequence generated). The authors apologize for this detail. read full comment
Comment on: Rochet et al. BMC Evolutionary Biology, 11:40
Typing error in Table 2 (Werner Mayer, 27 January 2011)
Upon reading the final version of Table 2 of our article I noticed the presence of a typing error. In row "Ppa-cel-1", column "synonymous substitutions" the figures read "0-1.8%" but should correctly be "0-8.1%". This correction should be brought to the attention of the readers of the article.
Werner E. Mayer
read full comment
Comment on: Mayer et al. BMC Evolutionary Biology, 11:13
A missing link in Dermaptera evolution (Dong Ren, 07 December 2010)
Evolutional history and origin of Dermaptera have been in contention, with dramatically different viewpoints by contemporary authors. It is suggested that the oldest Dermaptera might possibly be traced back to the Late Triassic–Early Jurassic and they had divided into Archidermaptera and (Eodermaptera+Neodermaptera) in the Middle Jurassic. read full comment
Comment on: Zhao et al. BMC Evolutionary Biology, 10:344
Note from the authors (Lars Podsiadlowski, 12 November 2010)
After publication of our manuscript in a preliminary form, it was brought to our attention that there is good evidence that the partial mitogenomic sequence assigned in GenBank to Nemertoderma westbladi (Nemertodermatida, GenBank AY228758) is in fact a mollusc sequence, likely due to DNA contamination presumably not detected by the authors of the original paper. To our knowledge this contamination has not been made public yet, nor has the GenBank accession been removed or amended; this task does not fall among our responsibilities. Nevertheless, we are concerned that inclusion of a partial and long-branched molluscan mitogenomic sequence has had effects on the phylogenetic analyses we performed, thus questioning the phylogenetic implications made in the publication at hand. We will soon... read full comment
Comment on: Mwinyi et al. BMC Evolutionary Biology, 10:309
Difficult to distinguish between new and old data (Tudor Borza, 27 October 2010)
The paper “Genomic organization and gene expression of the multiple globins in Atlantic cod: conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters” by Wetten et al.  presents data on Atlantic cod globin genes, the expression pattern of some of these genes (i.e., of hemoglobin genes), and discuss the genomic context of globin genes.
A closer inspection of this paper reveals that a significant amount of data is presented in a way that makes the distinction between new data, and already published data, extremely difficult for most readers.
To substantiate this observation this comment will be focused on:
1. The fact that the 9 Atlantic cod hemoglobin (Hb) genes, reported and discussed by Wetten et... read full comment
Comment on: Wetten et al. BMC Evolutionary Biology, 10:315
The corresponding author has since published the cleavage of DSPP by BMP1. (larry fisher, 12 October 2010)
Corresponding author (Fisher) has since published proof that mouse DSPP is cleaved by BMP1 at the expected MQXDDP motif as discussed in the above publication. (Dentin sialophosphoprotein (DSPP) is cleaved into its two natural dentin matrix products by three isoforms of bone morphogenetic protein-1 (BMP1). von Marschall Z, Fisher LW. Matrix Biol. 2010 May;29(4):295-303.) read full comment
Comment on: McKnight et al. BMC Evolutionary Biology, 9:299
Typographical change (Dorothee Huchon, 05 October 2010)
In the Discussion section, in the sentence:
"This suggests that “standard” barcoding primers might not be adapted for the sponge and cnidarian species that share introns 714 and 870."
870 should be replaced by 723 read full comment
Comment on: Szitenberg et al. BMC Evolutionary Biology, 10:288
Another possible explanation for unusual range of species (Brig Klyce, 16 July 2010)
You wrote, "the range of species in which mutation of the ARGFX locus is found do not form a monophyletic group to the exclusion of humans. There are several possible explanations for this unusual pattern." Then you list four possibilities.
I think you omitted an important one, horizontal gene transfer. This also could account for the unusual distribution. read full comment
Comment on: Li et al. BMC Evolutionary Biology, 10:182
Error in e-mail (Ji-Rui Wang, 05 July 2010)
The e-mail for YM Wei should be email@example.com read full comment
Comment on: Wang et al. BMC Evolutionary Biology, 10:170
Other similar works (Peter Campbell, 26 May 2010)
Nice paper. It is a proof of concept experiment using Drosophila sibling species to show that MALDI-MS can be used to distinguish small animals, not just the bacteria for which the method was developed originally. The authors were unaware of any similar prior work. In fact I published a similar though less detailed proof of concept experiment with Drosophila in 2005. Another paper using aphids appeared at almost exactly the same time.
Systematic Entomology (2005) 30, 186-190.
Entomologia Experimentalis et Applicata (2005) 117, 243-247.
Just for the record ;) read full comment
Comment on: Feltens et al. BMC Evolutionary Biology, 10:95