Fossil Phylogeny Research Articles

A new method for testing evolutionary rate variation and shifts in phenotypic evolution

Abstract Quantifying phenotypic evolutionary rates and their variation across phylogenetic trees is a major issue in evolutionary biology. A number of phylogenetic comparative methods (PCMs) currently perform such task. However, available PCMs can locate rate shifts pertaining to entire portions of the phylogeny, but not those expected to occur at the level of individual species and lineages, such as with the idea that body size changes more rapidly in insular vertebrates. Still, most PCMs cannot deal with fossil phylogenies, albeit fossils provide highly desirable information when it comes to understand trait variation and evolution. We developed a PCM based on phylogenetic ridge regression, which we named RRphylo, which assigns an evolutionary rate to each branch of the phylogeny, and is designed to locate rate shifts relating to entire clades, as well as to unrelated tree tips. We tested RRphylo on simulated trees and data to assess its performance under different conditions. Then, we repeated its application with two real case scenarios, the evolution of flight in ornithodirans and mammals and body size evolution in insular mammals, which are usually subsumed to evolve under different range regimes than terrestrial and continental species respectively. RRphylo performs well across all different conditions. The simulation experiments demonstrated it has low Type I and Type II error rate. We found significant evidence that flight accelerates the rate of body size evolution in vertebrates, and that the acquisition of very large body size slows down the rate. Still, insular mammals body size evolution is not faster than in continental species. RRphylo is a new PCM ideal to estimate variation and shift in the rate of phenotypic evolution with fossil data. In addition to testing evolutionary rate variation, it is open to a variety of further questions, such as the evolution of rates in time, the estimation of ancestral states and the estimation of phenotypic trends over time.

Biostratigraphic Problems Generated by Deep Sea Coring--Biosystematic Analysis, Evolutionary Species, and Non-Validity of Lineage Zones: ABSTRACT

Recent availability of stratigraphically continuous and hiatus-free sequences of pelagic sediment in deep sea cores have encouraged biostratigraphers to interpret lineages of oceanic microfossils from a viewpoint of gradual phyletic evolution. A few taxa do show anagenetic evolution, but the excellent stratigraphic record obtained from deep sea coring reveals that the overwhelming majority of species show only cladogenetic evolution with no gradual speciation. Biostratigraphers nevertheless persist in recognizing ancestral-descendant relations whenever possible, and arbitrary limits must therefore be applied when an evolving lineage is divided. This typological practice may be good biostratigraphy, but it is poor biosystematics. Phyletic biohorizons and lineage zones are explicitly defined and recognized by evolutionary criteria. For interpretation, these horizons and zones must rely on notions of phyletic gradualism and ancestor-descendant relations. These notions must rely on an evolutionary theory to allow their inference. However, biostratigraphy should not rely on evolutionary theory since biostratigraphy is the means by which we correlate strata to test evolutionary hypotheses about patterns of fossil phylogeny. For good biostratigraphic practice, evolutionary species should be recognized as single lineages without arbitrary and typological subdivision. Biosystematic analysis should begin with a cladogenetic analysis which infers taxon relations from characters exhibiting shared derived similarities. Classification should immediately follow to preserve the monophyletic relations of the clades. This system results in universal and timeless taxonomic hypotheses which are potentially falsifiable and thus scientifically testable. A biozonation based on such taxa is independent of evolutionary theory. Untestable assumptions and ad hoc hypotheses of ancestral-descendant relations and gradual speciation, such as must be used to recognize phyletic biohorizons and lineage zones, are unnecessary. End_of_Article - Last_Page 781------------