Proposal (191) to South American Classification Committee
Reassign the seven species currently assigned to the genus Oceanodroma to different genera
The current SACC Checklist recognises seven species within the genus Oceanodroma Reichenbach 1853. In a separate proposal, we have suggested that the genus Oceanodroma Reichenbach 1853 become a junior synonym of Hydrobates Boie 1822. If this proposal is accepted, the question arises of what generic names should be given to the seven species on the SACC Checklist.
Penhallurick and Wink carried out an analysis using Bayesian Inference (Mr Bayes3.1) of 95 taxa within the Procellariiformes.
We used PAUP (Swofford 1998) and ModelTest (Posada and Crandall 1998) to analyse the substitution patterns in a cytochrome-b data set against 56 different models of DNA evolution. We used the Akaike Information Criterion (AIC). The model selected was GTR+I+G.
We used Bayesian inference and Markov Chain Monte Carlo (mcmc) with Metropolis coupling for estimating phylogenetic hypotheses from DNA data. The model of nucleotide substitution used was the GTR model, following the results of ModelTest mentioned above. Thus, Nst was set to 6 and Rates to Invgamma. In relation to prior distributions, we used a flat Dirichlet for both Revmatpr and Statefreqpr. Ronquist et al. (2005) stated that use of the default settings is appropriate if we want to estimate these parameters from the data assuming no prior knowledge about their values. After three million generations, the average standard deviation of split frequencies was 0.008673. The mean of the 13 Potential Scale Reduction Factor (PSRF) figures was 1.002 (SD 0.003). We give, as Figure 1, a plot of the generation versus the log probability of the data (the log likelihood values). The plot approximates "white noise". All the data just cited support the validity of the analysis.
Figure 1. Plot of generation versus the log probability of the data (the log likelihood values) for the MrBayes3.1 analysis of the data
Figure 2. Phylogeny of all Procellariiformes
Bayesian Inference Tree. This represents a 50% majority rule consensus tree. Posterior Probability values are indicated, usually to the right of the nodes, but occasionally, for reasons of space, to the left.
Figure 3. displays that section of Figure 2 containing the storm-petrels
Table 1 displays both Tamura-Nei distance data, below the diagonal, and distances for bases involved in amino acid coding, above the diagonal, for the storm-petrel taxa analysed.
Note: All of these documents can be found at the author's website:
Click on Enter, and then on "SACC Documents" at the bottom of the menu on the left.
Figure 1 can be found under "Mr Bayes Plot"
Figure 2 under "Mr Bayes tree for Procellariiformes"
Figure 3 under "Mr Bayes subtree for Storm-Petrels"
and Table 1 under "Tamura-Nei and Amino Acid Distance matrix for Storm-Petrels"
At an earlier stage of this checklist, Van Remsen asked in a comment whether, if Oceanodroma was to become a junior synonym of Hydrobates, all of the taxa currently placed in Oceanodroma, should simply be placed in Hydrobates. We will now give reasons for recognising four distinct genera within the Hydrobatini.
o Within the Hydrobatini, Figures 2 and 3 show a posterior probability of 1.00 for the inclusion of Oceanodroma castro (Harcourt 1851) Band-rumped Storm-Petrel within this group.
o Also within that group, there is 1.00 posterior probability for the alignment of Hydrobates pelagicus (Linnaeus 1758) European Storm-Petrel with Oceanodroma furcata (J. F. Gmelin 1789) Fork-tailed Storm-Petrel.
o The alignment of Halocyptena microsoma Coues 1864 Least Storm-Petrel with Oceanodroma tethys (Bonaparte 1852) Wedge-rumped Storm-Petrel and Oceanodroma melania (Bonaparte 1854) Black Storm-Petrel has 1.00 posterior probability in Figures 2 and 3.
o The alignment of Oceanodroma leucorhoa (Vieillot 1818) Leach's Storm-Petrel with Oceanodroma tristrami Salvin 1896 Tristram's Storm-Petrel has 1.00 posterior probability.
We also argued that the distance data supported the recognition of distinct genera within each of these groups, although there has been a general bias against using distance data to make taxonomic judgments. Relevant here are the remarks of Helbig et al. (2002). On the role of nucleotide sequences in species judgments, Helbig et al. (2002: stated: "Molecular divergence is not a character (a particular sequence is), but sequence divergence measures can be used as an objective measure of overall divergence in comparative analyses. Molecular divergence, although not linearly correlated with phenotypic divergence, is proportional to the time that has elapsed since two taxa diverged from a common ancestor and thus gives a rough indication of how likely it is that reproductive incompatibilities have evolved between the two taxa." (Emphasis added). We note the criteria outlined in this paper have been adopted by the Taxonomic Sub-Committee of the British Ornithologists" Union Records Committee (Sangster et al. 2004); and that the Taxonomic Advisory Committee in relation to the Agreement on the conservation of albatrosses and petrels had as the first of its proposed Plan of Action for the Taxonomy Working Group (Available at http://www.acap.aq/index.php/content/download/482/1525/file/ACAP%20AC1%20Doc%2012%20Taxonomy.pdf): "Consider adopting the model presented by Helbig et al. (2002) · to the taxa listed in the ACAP agreement".
We remind readers that in Penhallurick and Wink (2004) we stated: "Protein distances appear to be almost linear with time." In that paper, we also stated in the caption to Figure 1: "A split of amniotes (reptiles, birds, mammals) is assumed to have taken place about 335 mio years ago; the split between bird and mammal lineages 310 mio years ago (Hedges et al., 1996)." Grauer and Martin (2004), kindly brought to our attention by Van Remsen (pers. comm.), argued that the date of 310 mya for the divergence date of diapsid reptiles and synapsid reptiles involved erroneous precision, and that the date should be more accurately expressed as 338 to 288 mya. If we divide the 34.1% divergence between the two groups mentioned above by 338, we get a rate of 0.10 pmy. If we divide it by 288 pmy, we get a rate of 0.12 pmy.
The mean Tamura-Nei (TN) distance between castro and other taxa in the other members of the Hydrobatini is 13.6112 (SD 0.3072); the mean amino acid distance (AA) is 4.9433 (SD 1.0795). The mean TN distance between [leucorhoa and tristrami] and the group consisting of [microsoma, tethys and melania] plus [pelagicus and furcata] is 12.1714 (SD 0.8450) with a mean AA distance of 3.61 (SD 0.8627). Finally, the mean TN distance between the [microsoma, tethys and melania] group and the [pelagicus and furcata] group is 11.7331, with an AA mean of 2.36. These figures are all significantly larger than the within-group means for all four groups (TN 8.6769, SD 0.2028; mean AA distance 2.6757 SD 1.3231).
If we examine the between-group figures for genera within the Oceanitini, we find that they are generally significantly lower than the between-group figures within the Hydrobatini: between oceanicus and nereis, marina, Grallaria plus tropica TN 10.6510 (SD 1.0213);mean AA distance 3.9175 (SD 1.0384); nereis to marina, grallaria and tropica TN 11.0391 (SD 0.3442); mean AA distance 4.3033 (SD 0.2750); and thirdly marina to grallaria and tropica TN 10.9538 (SD 1.6845); mean AA distance 3.7550 (SD 0.3889). The final piece of evidence is that the within-group figures within the Hydrobatini are generally less than those between distinct genera with the Oceanitini, and comparable to the within-group figures within the Hydrobatini. The clear implication of this is that since all four groups within the Hydrobatini are strongly supported by posterior probability figures(1.00) in Figures 2 and 3, each should be recognised as a distinct genus.
Thus, we offer our analysis of storm-petrel genera:
Within Hydrobates Boie 1822
1. Hydrobates pelagicus (Linnaeus 1758) European Storm-Petrel
2. Hydrobates furcatus (J. F. Gmelin 1789) Fork-tailed Storm-Petrel
within Cymochorea Coues 1864:
3. Cymochorea leucorhoa (Vieillot 1818) Leach's Storm-Petrel
4. Cymochorea tristrami (Salvin 1896) Tristram's Storm-Petrel
We also place four other taxa in this genus, giving:
5. Cymochorea monorhis (Swinhoe 1867) Swinhoe's Storm-Petrel tristrami is assigned by Sibley and Monroe (1990) to the markhami superspecies, again with the comment: 'May be conspecific with markhami.' On this basis, markhami will also be assigned to Cymochorea.
6. Cymochorea markhami Salvin 1883 Markham's Storm-Petrel
7. Cymochorea homochroa Coues 1864 Ashy Storm-Petrel
8. Cymochorea hornbyi (G. R. Gray 1854) Ringed Storm-Petrel
We lack data from O. homochroa (Coues 1864) Ashy Storm-Petrel, of the coast of California and the Pacific coast of Mexico, and O. hornbyi (G. R. Gray 1854) Ringed Storm-Petrel, of the Pacific coast of South America from Peru to Chile. All recent species sequences have placed these two species between O. matsudairae and O. furcata (see Jouanin and Mougin in Mayr and Cottrell 1979: 117; Sibley and Monroe 1990: 330; and Carboneras in del Hoyo et al. 1992: 271). The last-named source also says of O. homochroa, though without any further explanation, 'May form superspecies with O. monorhis and O. leucorhoa.' (ibid.) If this suggestion is correct, we would have Cymochorea homochroa and probably also Cymochorea hornbyi.
within Halocyptena Coues 1864:
9. Halocyptena microsoma Coues 1864 Least Storm-Petrel
10. Halocyptena tethys (Bonaparte 1852) Wedge-rumped Storm-Petrel
11. Halocyptena melania (Bonaparte 1854) Black Storm-Petrel
12. Halocyptena matsudairae (Nagamichi Kuroda 1922) Matsudaira's Storm-Petrel
Finally, we find 1.00 posterior probabilities support for the alignment of castro with the rest of the Oceanitini. The only available name is Thalobata Mathews 1943, which has Thalassidroma castro Harcourt 1851, as its type. Thus, we propose:
13. Thalobata castro (Harcourt 1851) Band-rumped Storm-Petrel
This will require the following changes in generic names for taxa within the South American Checklist:
Oceanodroma microsoma (Coues 1864) Least Storm-Petrel to become Halocyptena microsoma Coues 1864
Oceanodroma tethys (Bonaparte 1852) Wedge-rumped Storm-Petrel to become Halocyptena tethys (Bonaparte 1852)
Oceanodroma melania (Bonaparte 1854) Black Storm-Petrel to become Halocyptena melania (Bonaparte 1854)
Oceanodroma castro (Harcourt 1851) Band-rumped Storm-Petrel to become Thalobata castro (Harcourt 1851)
Oceanodroma leucorhoa (Vieillot 1818) Leach's Storm-Petrel to become Cymochorea leucorhoa (Vieillot 1818)
Oceanodroma markhami (Salvin 1883) Markham's Storm-Petrel to become Cymochorea markhami Salvin 1883.
Oceanodroma hornbyi (G. R. Gray 1854) Ringed Storm-Petrel to become Cymochorea hornbyi (G. R. Gray 1854)
First meeting of the Advisory Committee in relation to the Agreement on the conservation of albatrosses and petrels (Available at http://www.acap.aq/index.php/content/download/482/1525/file/ACAP%20AC1%20Doc%2012%20Taxonomy.pdf) Accessed 01/11/05
Grauer, D. and Martin, W. (2004). Reading the Entrails of Chickens: Molecular Timescales of Evolution and the Illusion of Precision. Trends in Genetics 20 (2), 80-86.
Hedges, S. B., Parker, H. P., Sibley, C. G. and Kumar, S. (1996). Continental breakup and the ordinal diversification of birds and mammals. Nature 381, 226-229.
Helbig, A. J., Knox, A. G., Parkin, D. T., Sangster, G. and Collinson, M. (2002) Guidelines for assigning species rank. Ibis 144, 518-525.
del Hoyo, J., Elliott, A. and Sargatal, J. eds. (1992) 'Handbook of the Birds of the World', Vol. 1. (Lynx Edicions, Barcelona).
Mayr, E. and Cottrell, G. W. (1979) 'Checklist of Birds of the World'. Vol.1, 2nd edn. (Museum of Comparative Zoology, Cambridge, Mass.)
Penhallurick, J. M and Wink, M. (2004) Analysis of the taxonomy and nomenclature of the Procellariiformes based on complete nucleotide sequences of the mitochondrial cytochrome-b gene. Emu 104, 125-47.
Posada, D. and Crandall, K. A. (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-88.
Ronquist, F., Huelsenbeck, J. P. and van der Mark, P. (2005) "MrBayes 3.1 Manual. Draft 26/05/2005". Available at: http://mrbayes.csit.fsu.edu/manual.php Accessed 1/11/05
Sangster, G., Collinson, M., Helbig, A. J., Knox, A. G. and Parkin, D. T. (2004) Taxonomic Recommendations for British Birds: Second Report. Ibis146, 153-157.
Sibley, C. G. and Monroe, B. L. Jr. (1990) "Distribution and taxonomy of birds of the world" (Yale University Press, New Haven and London.)
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John Penhallurick, November 2005
Comments from Stiles: "[190 and 191] are linked, such that a YES vote on 190 implies a YES on 191 as well. So far as it goes, the genetic evidence appears to favor the proposals, so a tentative YES to both. My main caveat is that only one gene was sequenced: is this sufficient?"
Comments from Remsen: "NO same comments as in 190 -- I strongly suspect that the Penhallurick-Wink data reveal the true phylogeny of the Hydrobatidae; certainly, their cyt-b tree is consistent with the traditional subfamily structure of the family based on traditional characters. Nonetheless, my personal policy on changes in classification is ... or tries to be ... based on congruence of two or more "data sets", e.g., two genes show same signal within the same paper, or two separate papers show same genetic results using different genes, or two sets of independent phenotypic characters shows the same thing, or any partial combination of the above. The guiding principal is that congruence among independent data sets gives me confidence that the results reveal true phylogeny, whereas I treat a single character as a phylogenetic hypothesis that should spawn additional testing. I doubt that I've been consistent in the application of this "policy", but I think when I've voted for a change based on 1 character, other characters that may not have been formerly analyzed are nonetheless consistent with the change. In this case, we're dealing with placing in synonymy the largest and most familiar genus name in the family, forcing the resurrection of older generic names, and so before making such a 'drastic' change to the classification, I eagerly await a second data set that supports this change. I think we should make sure we get this right before an overhaul of the generic boundaries within the family. As in many groups of birds that are superficially similar in their lack of size and plumage diversity, I would be surprised if the currently broadly defined genera do not indeed mask genetic divergence (beyond cyt b) and marked ecological/behavioral differences worthy of generic recognition, and so I look forward to any additional analyses that would sway my conservative vote, including existing data in the seabird literature."
Comments solicited by Remsen from Dr. Chris Witt, MVZ, UC Berkeley: "The cytochrome b phylogeny could be incorrect as a result of hybridization, incomplete lineage sorting, laboratory mistakes, or problems with the phylogenetic analysis. If the Bayesian posterior probabilities at each node are taken at face value, there are two potential changes that could be made: All of the species in that clade could be lumped into Hydrobates, or (2) the clade could be divided into up to 8 genera representing monophyletic mtDNA groups. Penhallurick opts for 4 genera, but his justification is based on cytochrome b genetic distances alone. That is inadequate (see above). Furthermore, If he had sampled cytochrome b from homochroa and hornbyi, would his taxonomic proposal be the same? It's not clear."
"In sum, the proposed changes would probably be fine, but their justification shouldn't hang on mtDNA data alone. In its current form, 191 is the most arbitrary of the three proposals [190-192] and, I think, least likely to withstand scrutiny provided by additional data and analyses. A proposal to call the whole Oceanodroma clade Hydrobates might be a viable alternative."
Comments from Robbins: "NO. To be consistent with my vote on proposal # 190, coupled with the comments by Witt, I vote NO."
Comments from Silva: "NO. To be consistent with my vote on proposal # 190."
Comments from Stiles: "I originally voted YES on this, but with the caveat that I was not sure that a single gene (cyt-b) was enough to justify such a change. The cogent arguments of Witt and the anonymous reviewer (and I hate anonymous reviewers!!) have convinced me that one gene is NOT enough; more evidence is required, and pending that evidence I will change my vote to NO."
Comments from Pacheco: "NO. Em consonância direta com o meu voto na proposta 190. Os resultados precisam ser refinados ou consubstanciados por iniciativa independente."
Comments from Zimmer: "NO, following the reasoning in Proposal #190, and additional comments by Chris Witt."
Comments from Jaramillo: "NO - See proposal 190, and comments from others. I will add that apart from those issues, I am troubled with how the species that were not sampled are treated. Markham's SP is put into Cymochorea based on comments by Sibley and Monroe, or is it based on their independent data? I am not clear. In any case, there are many similarities and also biogeographical issues that link Markham's to Black SP, I see that as an equally valid proposal. Now the treatment of Ashy and Ringed/Hornby's is even more troubling, and the uncertainty is clear in the proposal. I think we have to wait for more data."