--- Literatura Reciente sobre Filogenética Colección de referencias de artículos publicados recientemente. Esta lista se actualiza periódicamente tan pronto las versiones electrónicas están disponibles vía RSS. FEED Lo destacado: Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Pablo A. Goloboff, Santiago A. Catalano, J. Marcos Mirande, Claudia A. Szumik, J. Salvador Arias, Mari Källersjö and James S. Farris. Cladistics on line Abril27 2009 http://dx.doi.org/10.1111/j.1096-0031.2009.00255.x ABSTRACT Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process the largest phylogenetic data set ever analysed, consisting of molecular sequences and morphology for 73 060 eukaryotic taxa. The trees resulting from molecules alone display a high degree of congruence with the major taxonomic groups, with a small proportion of misplaced species; the combined data set retrieves these groups with even higher congruence. This shows that tree-calculation algorithms effectively retrieve phylogenetic history for very large data sets, and at the same time provides strong corroboration for the major eukaryotic lineages long recognized by taxonomists. ---------------------------------- Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches Stephen A Smith, Jeremy M Beaulieu and Michael J Donoghue BMC Evolutionary Biology 2009, Published: 11 February 2009 Abstract (provisional) Background Biology has increasingly recognized the necessity to build and utilize larger phylogenies to address broad evolutionary questions. Large phylogenies have facilitated the discovery of differential rates of molecular evolution between trees and herbs. They have helped us understand the diversification patterns of mammals, as well as the patterns of seed evolution. In addition to answering broad evolutionary questions, large phylogenies can be used to address conservation issues such as biodiversity hotspots and response to global change. Two major classes of methods have been employed to accomplish the large tree-building task: supertrees and supermatrices. Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists, making extremely large trees rare. Results Here we describe and demonstrate a modified supermatrix method termed mega-phylogeny that uses sequence databases, as well as taxonomic hierarchies, to make extremely large trees with somewhat denser matrices than supermatrices. The two major challenges facing large-scale supermatrix phylogenetics are assembling large data matrices from databases and reconstructing trees from those datasets. The mega-phylogeny approach addresses the former, as the latter is accomplished by employing recently developed methods that have greatly reduced the run time of large phylogeny construction. We present an algorithm that requires relatively little human intervention. The implemented algorithm is demonstrated with a dataset and phylogeny for Asterales (within Campanulidae) containing 4954 species and 12,033 sites and an rbcL matrix for green plants (Viridiplantae) with 13,533 species and 1,401 sites. Conclusions By examining much larger phylogenies, patterns emerge that were otherwise unseen. The phylogeny of Viridiplantae successfully reconstructs major relationships of vascular plants that previously required many more genes. These demonstrations underscore the importance of using large phylogenies to uncover important evolutionary patterns and we present a fast and simple method for constructing these phylogenies. ------------------------ WHY DOES A METHOD THAT FAILS CONTINUE TO BE USED? L. Lacey Knowles. KEYWORDS Biogeography • demographic history • historical inference • nested-clade analysis • phylogeography ABSTRACT As a critical framework for addressing a diversity of evolutionary and ecological questions, any method that provides accurate and detailed phylogeographic inference would be embraced. What is difficult to understand is the continued use of a method that not only fails, but also has never been shown to work—nested clade analysis is applied widely even though the conditions under which the method will provide reliable results have not yet been demonstrated. This contradiction between performance and popularity is even more perplexing given the recent methodological and computational advances for making historical inferences, which include estimating population genetic parameters and testing different biogeographic scenarios. Here I briefly review the history of criticisms and rebuttals that focus specifically on the high rate of incorrect phylogeographic inference of nested-clade analysis, with the goal of understanding what drives its unfettered popularity. In this case, the appeal of what nested-clade analysis claims to do—not what the method actually achieves—appears to explain its paradoxical status as a favorite method that fails. What a method promises, as opposed to how it performs, must be considered separately when evaluating whether the method represents a valuable tool for historical inference. ------------------------ The Austronesian Basic Vocabulary Database: from bioinformatics to lexomics (Provisional PDF) ------------------------------- ‘Total evidence’ in phylogenetic systematics Olivier Rieppel Online: Wednesday, August 06, 2008 Abstract Taking its clues from Popperian philosophy of science, cladistics adopted a number of assumptions of the empiricist tradition. These include the identification of a dichotomy between observation reports and theoretical statements and its subsequent abandonment on the basis of the insight that all observation reports are theory-laden. The neglect of the ‘context of discovery’, which is the step of theory (hypothesis) generation. The emphasis on coherentism in the ‘context of justification’, which is the step of evaluation of the relative merits of alternative theories. The appeal to a total evidence approach in phylogenetic inference. And finally, a silence about causation, which results in an instrumentalist approach to phylogeny reconstruction. This paper explores how these empiricist assumptions are embedded in phylogenetic systematics, and why these assumptions are problematic for cladists (or any taxonomists). Keywords K. R. Popper - Systematics - Total evidence - Direct optimization ------------------------------- Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution. ------------------------------- Weighting against homoplasy improves phylogenetic analysis of morphological data sets Pablo A. Goloboff, James M. Carpenter, J. Salvador Arias and Daniel Rafael Miranda Esquivel Abstract The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well-supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion ⁄ exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy-weighting methods) on 70 morphological data sets (with 50–170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets.
Simon J. Greenhill, Robert Blust and Russell D. Gray
Publication Date: 15 Oct 2008
Evolutionary Bioinformatics 2008:4
Simon J. Greenhill, Robert Blust, Russell D. Gray
Abstract
Phylogenetic methods have revolutionised evolutionary biology and have recently been applied to studies of linguistic and cultural evolution. However, the basic comparative data on the languages of the world required for these analyses is often widely dispersed in hard to obtain sources. Here we outline how our Austronesian Basic Vocabulary Database (ABVD) helps remedy this situation by collating wordlists from over 500 languages into one web-accessible database. We describe the technology underlying the ABVD and discuss the benefits that an evolutionary bioinformatic approach can provide. These include facilitating computational comparative linguistic research, answering questions about human prehistory, enabling syntheses with genetic data, and safe-guarding fragile linguistic information.
Rolando González-José, Ignacio Escapa, Walter A. Neves, Rubén Cúneo & Héctor M. Pucciarelli
Nature , | doi:10.1038/nature06891; Published online 4 May 2008.
Evolutionary novelties in the skeleton are usually expressed as changes in the timing of growth of features intrinsically integrated at different hierarchical levels of development1. As a consequence, most of the shape-traits observed across species do vary quantitatively rather than qualitatively2, in a multivariate space3 and in a modularized way4, 5. Because most phylogenetic analyses normally use discrete, hypothetically independent characters6, previous attempts have disregarded the phylogenetic signals potentially enclosed in the shape of morphological structures. When analysing low taxonomic levels, where most variation is quantitative in nature, solving basic requirements like the choice of characters and the capacity of using continuous, integrated traits is of crucial importance in recovering wider phylogenetic information. This is particularly relevant when analysing extinct lineages, where available data are limited to fossilized structures. Here we show that when continuous, multivariant and modularized characters are treated as such, cladistic analysis successfully solves relationships among main Homo taxa. Our attempt is based on a combination of cladistics, evolutionary-development-derived selection of characters, and geometric morphometrics methods. In contrast with previous cladistic analyses of hominid phylogeny, our method accounts for the quantitative nature of the traits, and respects their morphological integration patterns. Because complex phenotypes are observable across different taxonomic groups and are potentially informative about phylogenetic relationships, future analyses should point strongly to the incorporation of these types of trait.