Phylogenetic Analysis of Morphological Data (book review)

Journal of The History of Biology, 2008

In historical literature, Edouard van Beneden (1846-1910 is mostly remembered for his cytological discoveries. Less well known, however, is that he also introduced evolutionary morphology -and indeed evolutionary theory as such -in the Belgian academic world. The introduction of this research programme cannot be understood without taking both the international and the national context into account. It was clearly the German example of the Jena University that inspired van Beneden in his research interests. The actual launch of evolutionary morphology at his University of Lie`ge was, however, also connected with the dynamic of Belgian university reforms and the local rationale of creating a research ''school.'' Thanks to his networks, his mastering of the rhetoric of the ''new'' biology, his low ideological profile and his capitalising on the new academic e´lan in late-19th century Belgium, van Beneden managed to turn his programme into a local success from the 1870s onwards. Two decades later, however, the conceptual underpinnings of evolutionary morphology came under attack and the ''Van Beneden School'' lost much of its vitality. Despite this, van BenedenÕs evolutionary morphology was prototypical for the research that was to come. He was one of the first scientific heavyweights in Belgium to turn the university laboratory into a centre of scientific practice and the hub of a research school.

Handbook of Archaeological Theories, 2007

As Bentley et al. note in chapter 8 of this volume, Darwinian approaches to archaeology are rapidly gaining popularity, fueled in part by the recognition that cultural evolution can be fruitfully studied by adapting the analytical tools that evolutionary biologists and paleobiologists use to study biological evolution. The goal of this chapter is to illustrate how two of these methods, population genetics modeling and cladistic techniques of phylogenetic reconstruction, can be used to explain temporal and geographic variation in ...

Systematic Biology, 2001

Many aspects of morphological phylogenetics are controversial in the theoretical system- atics literature and yet are often poorly explained and justié ed in empirical studies. In this paper, I argue that most morphological characters describe variation that is fundamentally quantitative, re- gardless of whether they are coded qualitatively or quantitatively by systematists. Given this view, three fundamental problems in morphological

2001

Handbook of Paleoanthropology, 2007

We review Hennigian, maximum likelihood, and different Bayesian approaches to quantitative phylogenetic analysis and discuss their strengths and weaknesses. We also discuss various protocols for assessing the relative robustness of one's results. Hennigian approaches are justified by the Darwinian concepts of phylogenetic conservatism and the cohesion of homologies, embodied in Hennig's Auxiliary Principle, and applied using outgroup comparisons. They use parsimony as an epistemological tool. Maximum likelihood and Bayesian likelihood approaches are based on an ontological use of parsimony, choosing the simplest model possible to explain the data. All methods identify the same core of unambiguous data in any given data set, producing highly similar results. Disagreements most often stem from insufficient numbers of unambiguous characters in one or more of the data types. Appeals to Popperian philosophy cannot justify any kind of phylogenetic analysis, because they argue from effect to cause rather than cause to effect. Nor can any approach be justified by statistical consistency, because all may be consistent or inconsistent depending on the data being analyzed. If analyses based on different types of data or using different methods of phylogeny reconstruction, or some combination of both, do not produce the same results, more data are needed.

The Evolution of Texts: Confronting Stemmatological and Genetical Methods, ed. by C. Macé, Ph. V. Baret, A. Bozzi, and L. Cignoni (Linguistica Computazionale, 24), 2006, 89-108, 2006

Over these last few years, biologists and philologists have been working together using a common tool: phylogenetic methods. The use of these methods requires conceptual assumptions on the process of evolution of beings and texts, computerized databases, high capacities of calculation and a simplification of the representation of multidimensional data. In this paper, we will attempt to examine these different steps and to analyse the potential of biological based methods in the analysis of texts.

Netherlands Journal of Zoology, 1998

To reconstruct a phylogeny, data with sufficient resolving power are necessary. When morphological or molecular data fail this criterion, other data types are needed.

Evolution, 1996

Even though, from Darwin onwards, interisland evolution has been a cornerstone of evolutionary theory it has not been possible to determine to what extent this geographic variation reflects the phylogeny (e.g., pattern of island colonization) or ecogenetic adaptation to different ecological conditions on each island. Using the morphology of western Canary Island lacertids (Gal/otia gal/oti) as an example, a procedure is explored that gives a preliminary answer to this problem when there are a limited number of islands. The phylogenetic component (represented by patristic distances derived from 1005 mitochondrial DNA [mtDNA] base pairs) can be separated from two potential ecogenetic factors (environmental richness and climate) by partial Mantel tests. This reveals that, although these components interact, some characters are correlated primarily to biodiversity/paucity (e.g., size), others are correlated to wet and lush environments (e.g., dorsal pattern), and others are correlated primarily to the phylogeny (e.g., sexual leg markings). The former two correlations may be due to ecogenetic adaptation to current ecological conditions, wheras the latter reflects historical processes.

Phylogeography seeks to explain the geographic distribution of genetic lineages ...