Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference

Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference - Annual Review of Ecology, Evolution, and Systematics, 39(1):365 -
Abstract

Annual Review of Ecology, Evolution, and Systematics
Vol. 39: 365-385 (Volume publication date December 2008)
(doi:10.1146/annurev.ecolsys.38.091206.095752)
First published online as a Review in Advance on September 3, 2008

Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference

Daniel C. Fisher­

Museum of Paleontology and Department of Geological Sciences, University of Michigan, Ann Arbor, Michigan 48109; email: dcfisher@umich.edu

Debate has long simmered over whether data on the order of appearance of taxa in the stratigraphic record should play any role in analyses of phylogenetic relationships among those taxa. Critics argue that temporal data are in principle inapplicable to questions of cladistic relationship, but specific versions of this claim all seem flawed. Stratocladistics offers a methodological context (patterned after that of cladistics itself) within which temporal data participate along with conventional character data in selecting most-parsimonious hypotheses. Stratocladistics outperforms cladistics in tests based on simulated histories, and additional testing will be facilitated by new software automating stratocladistic searches. As with any body of data, we may decide to include or exclude temporal data for specific reasons, but the explanatory power of hypotheses that use both temporal and conventional character data exceeds that of hypotheses based on character data alone.

Phylogenetic Approaches to the Study of Extinction

Phylogenetic Approaches to the Study of Extinction - Annual Review of Ecology, Evolution, and Systematics, 39(1):301 -
Abstract

Annual Review of Ecology, Evolution, and Systematics
Vol. 39: 301-319 (Volume publication date December 2008)
(doi:10.1146/annurev-ecolsys-063008-102010)
First published online as a Review in Advance on August 29, 2008

Phylogenetic Approaches to the Study of Extinction

Andy Purvis­

Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom;

Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa

Morphological Integration and Developmental Modularity

Morphological Integration and Developmental Modularity - Annual Review of Ecology, Evolution, and Systematics, 39(1):115 - Abstract

Annual Review of Ecology, Evolution, and Systematics
Vol. 39: 115-132 (Volume publication date December 2008)
(doi:10.1146/annurev.ecolsys.37.091305.110054)
First published online as a Review in Advance on August 26, 2008

Morphological Integration and Developmental Modularity

Christian Peter Klingenberg­

Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom;

Biological systems, from molecular complexes to whole organisms and ecological interactions, tend to have a modular organization. Modules are sets of traits that are internally integrated by interactions among traits, but are relatively independent from other modules. The interactions within modules rely on different mechanisms, depending on the context of a study. For morphological traits, modularity occurs in developmental, genetic, functional, and evolutionary contexts. A range of methods for quantifying integration and modularity in morphological data is available, and a number of comparative and experimental designs can be used to compare the different contexts. How development produces covariation between traits can have substantial implications for understanding genetic variation and the potential for evolutionary change, but research in this area has only begun and many questions remain unanswered.