tag:blogger.com,1999:blog-8697616560977719586.post6054171485532269579..comments2023-10-28T01:53:23.721-07:00Comments on Systematics and Biogeography: (Not) Lars (Brundin)Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8697616560977719586.post-67750952643047320922009-10-09T00:38:16.838-07:002009-10-09T00:38:16.838-07:00You should read the paper by Packer et al., 2009.
...You should read the paper by Packer et al., 2009.<br /><br />It is a magnificent work that explains in detail and reasonable argumentation how DNA barcoding overcame morphology.<br /><br />Whilst morphologic descriptions may be necessary as scientific information on species, it is completely irrelevant for taxonomic purposes. DNA barcoding can address this task faster and with more accuracy, without the need of cumbersome taxonomic keys and decades of work.<br /><br />The paper can be downloaded from: <br /><br />http://dx.doi.org/10.1111/j.1755-0998.2009.02631.x<br /><br />http://www3.interscience.wiley.com/journal/122342773/abstractLarsnoreply@blogger.comtag:blogger.com,1999:blog-8697616560977719586.post-19801076478944605322009-09-21T22:01:38.873-07:002009-09-21T22:01:38.873-07:00Genetic barcoding, now that it is being used on a ...Genetic barcoding, now that it is being used on a wide scale, is showing just as many pitfalls and confusing pictures of evolution as, well, morphology. With paraphyletic and polyphyletic gene trees widespread (Funk & Omland 2003), classical morphology stops looking so "treacherous". Every caution Lars cites for morphology also applies to genes. And despite some initial propaganda, even partisans of barcoding no longer claim that barcodes will do anything significant to address the taxonomic impediment.<br />For some recent publications (excluding the outright polemics for or against barcoding) see also Little & Stevenson 2007, Meyer & Paulay 2005, and Song et al. 2008.<br /><br />Funk, D.J. and K. E. Omland. 2003. SPECIES-LEVEL PARAPHYLY AND POLYPHYLY:Frequency, Causes, and Consequences, withInsights from Animal Mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 2003. 34:397–423.<br /><br />Little,D.P. and D.W. Stevenson. 2007. A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23 (2007) 1–21.<br /><br /><br />Meyer CP, Paulay G. 2005. DNA barcoding: Error rates based on comprehensive sampling. PLoS Biol 3(12): e422.<br /><br />Song, H., J.E. Buhay,, M.F. Whiting, M.F., and Keith A. Crandall. 2008. Many species in one: DNA barcoding overestimates<br />the number of species when nuclear mitochondrial pseudogenes are coamplified. PNAS 105: 13486–13491.Wills Flowersnoreply@blogger.comtag:blogger.com,1999:blog-8697616560977719586.post-81702545669639688112009-09-20T19:55:11.012-07:002009-09-20T19:55:11.012-07:00As far as I can see, morphology has its role as a ...As far as I can see, morphology has its role as a descriptive tool. This includes morphology applied to developmental biology too. However, when one intents are to assess the evolutionary relationships among species, it requires data which can fulfill an objective inferential framework, or the error will be enormous.<br /><br />To this, genes suffice. <br /><br />But genes are data. They need to be analyzed according to robust methods which can provide an account on error measurement and that can handle all possible information, regardless on the researcher's subjectivity on homologies. This is where Maximum-Likelihood algorithms enter.<br /><br />In the context of Paleontology, however, DNA is rarely available, thus morphology can be used as a second-choice kind of data. But how can it be scored? Morphometric characters are indicated, as they can be converted to distance matrices.<br /><br />Obviously, morphological features are associated to phenotype evolution, and hold information on organismal natural history. But the amount of convergences and the subjectivity on descriptions is too large to be overlooked. Thus, only a few well-known and potentially inclusive characters can be used with confidence. But keep in mind that different morphological information will produce different trees. This is another major drawback of morphology. But it seems cladists will never agree!<br />For this matter, you should read the paper by Scotland et al. (2003)*.<br /><br />Genetic barcoding provides an efficient tool for taxonomists, since they can almost perfectly be used to identify known species and to estimate the occurrence of organisms yet unknown to science. Remember that morphology can be treacherous, as ecotypes and intraspecific polymorphism do exist! Furthermore, genetic barcoding, although more expensive than simple morphology-based taxonomy, can significantly address the issue of taxonomic impediment.<br /><br /><br /><br />*SCOTLAND, R. W., R. G. OLMSTEAD, AND J. R. BENNETT. 2003. Phylogeny<br />reconstruction: the role of morphology. Syst. Biol. 52:539-548.Larsnoreply@blogger.comtag:blogger.com,1999:blog-8697616560977719586.post-16918962176201666182009-09-20T02:04:56.723-07:002009-09-20T02:04:56.723-07:00Well, I'm glad that's settled! Can we proc...Well, I'm glad that's settled! Can we proceed to throw in the towel on comparative developmental biology, too? After all, since morphology is so subjective how can we be sure of anything in developmental biology? I'm guessing the solution to this problem will be 'genes', too?Anonymousnoreply@blogger.com