DANIEL P FAITHFRANK KOHLERLOUISE PUSLEDNIKJ.W.O. BALLARD...
5页
查看更多>>摘要：Mooi & Gill (2010) argued that careful character study and well-understood synapomorphies do not have the strong role that they deserve as the basis for evidence in phylogenetics. We agree, but suggest that the problem is even greater. Not only character synapomorphies, but also other forms of phylogenetic evidence, typically do not receive the critical assessment that would support phylogenetic inference. In this paper, our goal is to not simply to highlight problems but to suggest solutions. We will suggest that a stronger role for corroboration assessment in systematics could overcome these problems in phylogenetic inference.
查看更多>>摘要：All systematists should be just as comfortable examining and comparing museum specimens as they are at examining and comparing DNA sequences;...the future will favor...researchers who are not afraid to choose the best approach for any given phylogenetic puzzle - whether it means studying morphological or molecular variation, or both.—Hillis & Weins, 2000, p. 15. The molecular revolution in phylogenetic biology and its widespread application to fishes has in some ways complicated the task of teachingmy craft of ichthyology. Beginning students know nothing of the history of fish classifications, how they were created, how they have changed over the years or how and why they continue to change. On the first day of class I typically bring in the foureditions of Joe Nelson's classic Fishes of the World (Nelson, 1976, 1984, 1994, 2006) to show students that systematic ichthyology is a vibrant and dynamic science and that these are exciting times. Then I add that the latest of these encyclopedias of our current knowledge has for the most part not incorporated the more radical changes in our understanding of fish relationships suggested by many recent
查看更多>>摘要：All systematists should be just as comfortable examining and comparing museum specimens as they are at examining and comparing DNA sequences;...the future will favor...researchers who are not afraid to choose the best approach for any given phylogenetic puzzle - whether it means studying morphological or molecular variation, or both.—Hillis & Weins, 2000, p. 15. The molecular revolution in phylogenetic biology and its widespread application to fishes has in some ways complicated the task of teachingmy craft of ichthyology. Beginning students know nothing of the history of fish classifications, how they were created, how they have changed over the years or how and why they continue to change. On the first day of class I typically bring in the foureditions of Joe Nelson's classic Fishes of the World (Nelson, 1976, 1984, 1994, 2006) to show students that systematic ichthyology is a vibrant and dynamic science and that these are exciting times. Then I add that the latest of these encyclopedias of our current knowledge has for the most part not incorporated the more radical changes in our understanding of fish relationships suggested by many recent
MALTE C. EBACHMARCELO R. DE CARVALHODAVID M. WILLIAMS
5页
查看更多>>摘要：Mooi & Gill (2010) have prised open the cap of the molecular systematics vial and caused a debate to take-off in the ichthyological community. Molecular trees and their supporting evidence are the first two items to leave this Pandora's box, closely followed by DNA barcoding and DNA taxonomy. In short, the debate is fuelled by the nature of molecular data: can nucleotide sequences provide the necessary evidence for relationship? The majority (Wiley et al, 2011) believe that DNA contains informative data; however, in our view, they have failed to ascertain the truth of their claim. Not all data are informative. Data may provide supporting evidence, conflicting evidence, or no evidence at all. Assuming that all data are informative apriori to analysisis a theoretical position, not an empirical one. We claim that systematics is, quite the contrary, empirical, and relies on evidence rather than on implicit measurements of data. Consequently, this assertion leads back to the original question of evidence in molecular systematics, namely molecular homology.
MALTE C. EBACHMARCELO R. DE CARVALHODAVID M. WILLIAMS
5页
查看更多>>摘要：Mooi & Gill (2010) have prised open the cap of the molecular systematics vial and caused a debate to take-off in the ichthyological community. Molecular trees and their supporting evidence are the first two items to leave this Pandora's box, closely followed by DNA barcoding and DNA taxonomy. In short, the debate is fuelled by the nature of molecular data: can nucleotide sequences provide the necessary evidence for relationship? The majority (Wiley et al, 2011) believe that DNA contains informative data; however, in our view, they have failed to ascertain the truth of their claim. Not all data are informative. Data may provide supporting evidence, conflicting evidence, or no evidence at all. Assuming that all data are informative apriori to analysisis a theoretical position, not an empirical one. We claim that systematics is, quite the contrary, empirical, and relies on evidence rather than on implicit measurements of data. Consequently, this assertion leads back to the original question of evidence in molecular systematics, namely molecular homology.
查看更多>>摘要：In two recent papers Mooi & Gill (2010a, 2010b) stressed that the evaluation and discussion of character homologies and their significance as synapomorphies has disappeared from current molecular phylogenetic analyses in ichthyology (see Chakrabarty (2010) and Smith (2010) for a different perspective). Synapomorphies represent the evidence that allows us to postulate phylogenetic groupings under the paradigm of Hennig's (1950, 1966) phylogenetic systematics. Therefore, their absence would indeed indicate an absence of evidence and hence a reason for serious concern. In the following paragraphs we provide a brief review of the differences between morphological and molecular approaches in relation to the establishment of homology.
查看更多>>摘要：In a recent paper, Mooi & Gill (2010) raised various issues related to recent developments in molecular systematic ichthyology that they found alarming. They went so far as to call this a "crisis in fish systematics." They criticised the trend that alternative trees for the placement of a taxon in question are not critically discussed and the reason for the divergent positions is not adequately evaluated. They raise the important question "On what basis is one topology to be preferred over the other?"
查看更多>>摘要：The varied possibilities to interpret data about taxa, their interrelationships and their geographic distributions, may be seen as different methods of analysis of data of these kinds... Different methods, even applied to the same data, tend towards different results. In a historical sense, different and conflicting results—different histories— cannot all be true. At least some must be artifactual and, therefore, method-generated (Nelson & Ladiges, 2001: 389)
查看更多>>摘要：The Systematics Association (SA), a London based organisation dedicated to the promotion of systematic (comparative) biology in all its various aspects, was founded in May 1937. It is based on objectives set out for its earlier incarnation, the "Committee on Systematics in Relation to General Biology" (some relevant history can be found in Winsor 2000). That group's remit was, and the SA's still is, "to provide a forum for the discussion of the general theoretical and practical problems of taxonomy"(http://www.systass.org ; see also Nature 140:163, 1938).
查看更多>>摘要：The Connection between three ideas, resemblance as evidence of ancestry, was made long ago by Denis Diderot (1713-1784), a notable figure of the French enlightenment, the siecle des lumieres (Lovejoy, 1904: 325). In 1753 he provided an example of whattoday is termed "transformational homology" (Patterson, 1982: 36): "If one considers the animal kingdom, and particularly the mammals, there is not one that lacks the functions and the parts, particularly internal ones, that are entirely similar to theothers; so much so that it is easy to believe that there was a first prototype for all of them, for which nature merely elongated, shortened, transformed, multiplied, or obliterated certain organs. Imagine the fingers of the hand united, and the substance of the nails so abundant that it extends over the whole; then in place of the hand of a man, you have the foot of a horse."
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