The reform of palaeontology and the rise of biogeography – 25 years after ‘ontogeny, phylogeny, paleontology and the biogenetic law’ (Nelson, 1978)

Williams, David M.; Ebach, Malte C.

doi:10.1111/j.1365-2699.2004.01063.x

Cited by 42 publications

(11 citation statements)

References 139 publications

(179 reference statements)

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“…In contrast, panbiogeography (Croizat, 1964; Craw et al., 1999) has insisted on the distinction between age of being and age of fossilization , and the idea that fossils are ancestors has been severely criticized by cladists (Gee, 1999; Williams and Ebach, 2004).…”

Section: Correlating the Age Of Taxa With The Age Of The Oldest Knownmentioning

confidence: 99%

Dating nodes on molecular phylogenies: a critique of molecular biogeography

2005

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Taxa have been dated using three methods: equating their age with the age of the oldest known fossil, with the age of strata the taxa are endemic to, and with the age of paleogeographic events. All three methods have been adopted as methods of dating nodes in molecular phylogenies. The first method has been the most popular, but both this and the second method involve serious difficulties. Studies often, correctly, introduce oldest known fossils as providing minimum ages for divergences. However, in the actual analyses these ages, and ages derived from them, are often treated as absolute ages and earlier geological events are deemed irrelevant to the phylogeny. In fact, only younger geological events can be irrelevant. Studies correlating the age of nodes with age of volcanic islands often overlook the fact that these islands have been produced at subduction zones or hot spots where small, individually ephemeral islands are constantly being produced and disappearing, and a metapopulation can survive indefinitely. Correlating the age of taxa with that of associated paleogeographic events is probably the most promising method but has often been used in a simplistic way, for example in assuming that all divergence across the Isthmus of Panama dates to its final rise. Most workers now agree that a global molecular clock does not exist, and that rates can change between lineages and within a lineage over time. New methods of estimating branch lengths do not assume a strict clock, but the number of models for molecular evolution is then effectively infinite. Problems with calibrating the nodes, as well as with substitution models, mean that phylogeography's claim to be able to test between vicariance and dispersal is not justified.

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Section: Correlating the Age Of Taxa With The Age Of The Oldest Knownmentioning

confidence: 99%

Dating nodes on molecular phylogenies: a critique of molecular biogeography

2005

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“…In this context, phylogeny undisputedly assumes (Crisci, 2001) cladistics as the common language of comparative biology [systematics, biogeography, embryology and palaeontology (Nelson & Platnick, 1981), or as a three‐fold parallelism uniting ontogeny, morphology and geography (Nelson, 1989) – see also Williams & Ebach (2004), for a historical explanation of the subject]. However, historical biogeography can be applied to either areas (area relationship approach) or species (taxon relationship approach) (Brooks & van Veller, 2003), so historical biogeography cannot be completely anchored in or underlined by phylogenies of organisms (see more on this discussion below).…”

Section: What Is Pae?mentioning

confidence: 99%

Misconceptions about parsimony analysis of endemicity

Nihei¹

2006

Journal of Biogeography

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Parsimony analysis of endemicity (PAE) has been widely criticized in the recent literature based on methodology rather than on theory. Here I argue that most of the criticisms of PAE result from confusion between the dynamic and static approaches of PAE, by both users and critics of the method. Originally, PAE (the dynamic approach) was proposed primarily for historical comparisons of biotic distributions based on geological and stratigraphical information; that is, the stratigraphical record of the biota within two or more horizons was used to evaluate changes (layer by layer) in their distributional patterns. This led to an analysis of the biota throughout space and through time. On the other hand, the static approach excluded the temporal component and based the analysis on a single geological horizon. Most problems exemplified and discussed in the literature refer to the static approach. In addition to this defence of the original PAE, I present some new criticisms regarding the application of PAE using artificially delimited areas (for example areas defined by geopolitical boundaries), which may lead to incorrect interpretations. Recently, several variations of static PAE have appeared: some designed to accommodate ecological data (e.g. parsimony analysis of distributions – PAD); others that incorporate phylogenetic content (e.g. cladistic analysis of distributions and endemism – CADE); and some that have been integrated with other historical methods (e.g. panbiogeography) in order to detect and evaluate hypotheses of biogeographical homologies. Biogeographers, both ecological and historical, should be aware of the problems and limitations of both dynamic and static PAE and evaluate new variations of PAE (PAD, CADE, etc.). Finally, I argue in favour of an independent and pluralist discipline of biogeography that treats biogeography as related to systematics but not dependent on it, as some scholars have assumed.

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“…A[TT] relates certain taxa but not others). Using the threefold parallelism of Agassiz (1859; Williams and Ebach, 2004) may be a step back into the ancient literature, but it is gigantic leap forward for comparative biology, an area that molecular systematics has avoided addressing. We believe that by introducing fundamental concepts like the threefold parallelism and morphological homology, molecular systematics can build up a theory that would serve as a foundation to finding molecular homologies.…”

Section: Citing Evidencementioning

confidence: 99%

Opening Pandora’s Molecular Box

Ebach

Carvalho

Williams

2011

Zootaxa

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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 analysis is 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.

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The reform of palaeontology and the rise of biogeography – 25 years after ‘ontogeny, phylogeny, paleontology and the biogenetic law’ (Nelson, 1978)

Cited by 42 publications

References 139 publications

Dating nodes on molecular phylogenies: a critique of molecular biogeography

Dating nodes on molecular phylogenies: a critique of molecular biogeography

Misconceptions about parsimony analysis of endemicity

Opening Pandora’s Molecular Box

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