IB 200B Principals of Phylogenetic Systematics Spring 2009Integrating Fossils into PhylogeniesThroughout the 20th century, the relationship between paleontology and evolutionary biology has been strained.Two common answers are: (1) the two fields have fundamentally different aims, and (2) the tensions arise out of disciplinary squabbles for funding and prestige.Principal differences between neontology and paleobiologyNeontological evolutionary Evolutionary paleobiologybiologyFocus of study Living organisms Fossil remains of organismsTemporal Shorter term: Typically longer term:perspective 10−2 – 103 years 103 – 107 yearsTheory Models of natural selection and Relies on broader neo-darwinianSpeciation, generally articulated theory; rarely uses populationin terms of population or genetic theory. Some distinctivelyquantitative genetics paleobiological theory(e.g., taphonomy)Methods Greater emphasis on Less emphasis onexperiments experimentsData Emphasizes genetic data Extremely limited access toand population structure genetic data and population structureJohn Maynard Smith (1920-2004) – British evolutionary biologist and geneticist; evolution of sex, game theory in evolution, and signaling theory.Smith, J. M. (1984). ""Paleontology at the high table.". Nature 309 (5967): 401-402. – Hennig Character phylogeny ( ).polarity“ . Criterion of geological character precedence If in a a monophyletic , group a particular character condition occurs only in older fossils and , another only in younger fossils then obviously the former is .”pleisomorphous and the latter the apomorphous condition .Hennig goes on to discuss paleontological methods of phylogenetic systematicsDuring much of the 19th and 20th centuries, palaeontology was often considered as fundamental for understanding relationships amongst extant taxa. . . . Then, in the late 1970s and early 1980s,with the advent of cladistics, the supremacy of fossils in phylogentic reconstruction was forcefully and successfully challenged. Colin Patterson (1981):(1) The distribution of traits among extinct taxa could be used to estimate sister group relationships, but the incompleteness of fossils makes fossils inherently less informative than extant taxa. In addition he argues that in practice. Thus as a practical matter including fossil data will rarely make major contributions to phylogeny reconstruction.(2) Fossils can be used to determine ancestor-descendant relationships. But suppose that species A and B are “sister taxa,” and all of A’s traits are ancestral relative to B’s, and species A both appears in and disappears from the fossil record before B. Would this justify the claim that A is the ancestor of B? While it is possible that A evolved directly into B, it is also possible that A and B are sister species that diverged from a common ancestor (C).Patterson concludes “that the widespread belief that fossils are the only, or best, means of determining evolutionary relationships is a myth” Patterson, C.: 1981, ‘Significance of Fossils in Determining Evolutionary Relationships’, Annual Review of Ecology and Systematics 12, 195–223.Resolution of long branches: Burgess Shale Arthropods.23Recent reviews suggest that fossil data are useful to:(1) determine the polarity of specific traits or to identify the root of anunrooted tree.(2) provide a more detailed reconstruction of the sequence of evolutionarychanges that led to novel traits.(3) re-assess initial hypotheses of homology or homoplasy.Although evolutionary systematics initially created a rift between paleobiological and neontological systematists, cladistics ultimately provided a set of methods that have been broadly accepted in both communities. Thus, the “cladistics revolution” contributed to the methodological unification of these fields.Stratigraphic DataCladistic analyses can conflict with the temporal information provided by the fossil record. Suppose that a cladistic analysis supports the hypothesis that A is the sister taxon to (BC). This analysis implies that A (or the lineage from the common ancestor of all three taxa to A) must have existed before the appearance of either B or C. What if A does not enter the fossil record until well after B and C? Is this evidence against the cladistic inference?Three responses to the integration of stratigraphic data into the fossil record.(1) Strict cladism relies solely on character data to determine the pattern ofbranching. Conflicts between stratigraphic and character data are thoughtto result from incompleteness in the fossil record.(2) Limited use of stratigraphic data. Stratigraphic data can be used as atiebreaker to decide between equally parsimonious cladograms (or toinfer a tree from a cladogram), but are never allowed to “over-ride”parsimony considerations. Primarily associated with Andrew Smith (BMNH)(3) Full incorporation of stratigraphic data. Several different methods4attempt to estimate phylogeny in light of both stratigraphic and characterdata. These methods sometimes accept less parsimonious cladograms inorder to gain better stratigraphic fit.Number 1 requires ad hoc assumptions about the fossil record. If you want to avoid ad hoc assumptions in your research then it makes sense to use stratigraphic evidence as a “tiebreaker” (i.e., to decide among equally parsimonious cladograms) Number 2 - Tie-breaker (Andrew Smith BMNH)5Stratophenetics (Phil Gingerrich UM)Stratophenetics favored by O’Keefe and Sander because:(1) The species are stratigraphically non-overlapping; they are never foundtogether.(2) 400 specimens were identified in this basin, including many complete skeletons. Given this quality of preservation, extending the range of N. edwardsii back in time (as in 6c) is an ad hoc assumption of incompleteness.(3) These two species are endemic to this basin. Appearance in the basin probably reflectsa real origination (not immigration) and their disappearance is best seen as either extinction or anagenesis (not emigration).6Number 3 - Full incorporation of stratigraphic data (Dan Fisher UM, Pete Wagner USNM, Ken Angielczyk IB & UCMP)The stratigraphic debt is equal to the number of intervals through which lineages must be extended, even though other species in the clade were observed during those intervals. This technique applies to range extensions and ghost lineages,
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