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Nomenclatural Acts (Dong Ren, 04 November 2014)

This published work and the nomenclatural acts it contains have been registered on ZooBank: LSID urn:lsid:zoobank.org:pub:4D2544F5-51D7-4FC7-B273-B03AE301E2EF   The Followings LSIDs are applied to taxa named in this publication:   Rectilyda Wang, Rasnitsyn, Shih & Ren, 2014 LSID urn:lsid:zoobank.org:act:9FED09A0-AD93-4F6E-98C3-E82E6D4CD2D6   Rectilyda sticta Wang, Rasnitsyn, Shih & Ren, 2014 LSID urn:lsid:zoobank.org:act:1DDCA3E8-AC84-4610-B820-BA14D4169665   These taxa are in compliance with the rules and regulations set out in the International Code for Zoological Nomenclature. read full comment

Comment on: Wang et al. BMC Evolutionary Biology, 14:131

Error in enzyme name (Joao Alves, 30 May 2014)

I have just noticed that we, somehow, had the wrong enzyme name for EC:1.1.1.3 in subsection "Methionine and cysteine" of "Results and discussion". The correct name, as present everywhere else in the paper, is "homoserine dehydrogenase" (and not "homocysteine methytransferase" as written). Not sure how that one slipped past us, since an EC number starting with 1 could never be a methyltransferase... Sorry for any inconvenience this switch might have caused. read full comment

Comment on: Alves et al. BMC Evolutionary Biology, 13:190

Update of the U6 phylogeny (Christopher Foote, 29 May 2014)

Comment posted on behalf of Dr Bernard Secher and his co-... read full comment

Comment on: Secher et al. BMC Evolutionary Biology, 14:109

Nomenclatural Acts (James Lamsdell, 25 March 2014)

This published work and the nomenclatural acts it contains have been registered on ZooBank: <a href='http://zoobank.org/References/5FDEADB6-754D-4BCE-8AE5-CC057ABD725'>http://zoobank.org/References/5FDEADB6-754D-4BCE-8AE5-... read full comment

Comment on: Lamsdell et al. BMC Evolutionary Biology, 13:98

Mistake (Eric Parmentier, 24 February 2014)

Figure 1: x-axis scale should be in cm read full comment

Comment on: Millot et al. BMC Evolutionary Biology, 14:24

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:

http://milkweedgenome.org


Matthew Parks
Aaron Liston
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:

JN236502-JN241549
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)


--Methods--

1)

Taxon Sampling
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."


2)

Phylogenetic analyses
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 [104].", 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)

Dear Sir,
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.
Sincerely,
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. [1] 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