Cladistics

Cladistics is a class of methods of biological classification that groups taxa hierarchically into discrete sets and subsets. This article presents the principles and concepts of cladistics and describes the principal analytical methods. The operations by which observations of organisms are coded for analysis are explained, followed by the methods for reconstructing the hierarchical relationships among taxa (usually expressed as branching diagrams termed cladograms). Statistics and principles for determining the degree of fit between data and cladograms are discussed, which permit choices to be made among competing cladograms.The attached document is the author(’s’) final submitted version of the journal article. You are advised to consult the publisher’s version if you wish to cite from it

Hints for families of GRBs improving the Hubble diagram

As soon as their extragalactic origins were established, the hope to make Gamma - Ray Bursts (GRBs) standardizeable candles to probe the very high - z universe has opened the search for scaling relations between redshift independent observable quantities and distance dependent ones. Although some remarkable success has been achieved, the empirical correlations thus found are still affected by a significant intrinsic scatter which downgrades the precision in the inferred GRBs Hubble diagram. We investigate here whether this scatter may come from fitting together objects belonging to intrinsically different classes. To this end, we rely on a cladistics analysis to partition GRBs in homogenous families according to their rest frame properties. Although the poor statistics prevent us from drawing a definitive answer, we find that both the intrinsic scatter and the coefficients of the $E_{peak}$\,-\,$E_{iso}$ and $E_{peak}$\,-\,$L$ correlations significantly change depending on which subsample is fitted. It turns out that the fit to the full sample leads to a scaling relation which approximately follows the diagonal of the region delimited by the fits to each homogenous class. We therefore argue that a preliminary identification of the class a GRB belongs to is necessary in order to select the right scaling relation to be used in order to not bias the distance determination and hence the Hubble diagram.Comment: 10 pages, 6 figures, 4 tables, accepted for publication on MNRA

Astrocladistics: Multivariate Evolutionary Analysis in Astrophysics

The Hubble tuning fork diagram, based on morphology and established in the 1930s, has always been the preferred scheme for classification of galaxies. However, the current large amount of data up to higher and higher redshifts asks for more sophisticated statistical approaches like multivariate analyses. Clustering analyses are still very confidential, and do not take into account the unavoidable characteristics in our Universe: evolution. Assuming branching evolution of galaxies as a 'transmission with modification', we have shown that the concepts and tools of phylogenetic systematics (cladistics) can be heuristically transposed to the case of galaxies. This approach that we call "astrocladistics", has now successfully been applied on several samples of galaxies and globular clusters. Maximum parsimony and distance-based approaches are the most popular methods to produce phylogenetic trees and, like most other studies, we had to discretize our variables. However, since astrophysical data are intrinsically continuous, we are contributing to the growing need for applying phylogenetic methods to continuous characters.Comment: Invited talk at the session: Astrostatistics (Statistical analysis of data related to Astronomy and Astrophysics

Barbaetis: A New Genus of Eastern Nearctic Mayflies (Ephemeroptera: Baetidae)

The new genus Barbaetis Waltz and McCafferty, and new species Barbaetis benfieldi Kennedy are described from larvae collected from the New River, Virginia. Barbaetis is easily told from Baetis by the presence of procoxal osmobranchia. Cladistics of B. benfieldi, related Pseudocloeon species, and the lutheri and pavidus complexes of Baetis are presented and indicate the need for further taxonomic revision. The habitat of B. benfieldi is described in terms of several ecological parameters. The new species demonstrates a univoltine life history with postembryonic development restricted to a short springtime period

Clustering with phylogenetic tools in astrophysics

Phylogenetic approaches are finding more and more applications outside the field of biology. Astrophysics is no exception since an overwhelming amount of multivariate data has appeared in the last twenty years or so. In particular, the diversification of galaxies throughout the evolution of the Universe quite naturally invokes phylogenetic approaches. We have demonstrated that Maximum Parsimony brings useful astrophysical results, and we now proceed toward the analyses of large datasets for galaxies. In this talk I present how we solve the major difficulties for this goal: the choice of the parameters, their discretization, and the analysis of a high number of objects with an unsupervised NP-hard classification technique like cladistics. 1. Introduction How do the galaxy form, and when? How did the galaxy evolve and transform themselves to create the diversity we observe? What are the progenitors to present-day galaxies? To answer these big questions, observations throughout the Universe and the physical modelisation are obvious tools. But between these, there is a key process, without which it would be impossible to extract some digestible information from the complexity of these systems. This is classification. One century ago, galaxies were discovered by Hubble. From images obtained in the visible range of wavelengths, he synthetised his observations through the usual process: classification. With only one parameter (the shape) that is qualitative and determined with the eye, he found four categories: ellipticals, spirals, barred spirals and irregulars. This is the famous Hubble classification. He later hypothetized relationships between these classes, building the Hubble Tuning Fork. The Hubble classification has been refined, notably by de Vaucouleurs, and is still used as the only global classification of galaxies. Even though the physical relationships proposed by Hubble are not retained any more, the Hubble Tuning Fork is nearly always used to represent the classification of the galaxy diversity under its new name the Hubble sequence (e.g. Delgado-Serrano, 2012). Its success is impressive and can be understood by its simplicity, even its beauty, and by the many correlations found between the morphology of galaxies and their other properties. And one must admit that there is no alternative up to now, even though both the Hubble classification and diagram have been recognised to be unsatisfactory. Among the most obvious flaws of this classification, one must mention its monovariate, qualitative, subjective and old-fashioned nature, as well as the difficulty to characterise the morphology of distant galaxies. The first two most significant multivariate studies were by Watanabe et al. (1985) and Whitmore (1984). Since the year 2005, the number of studies attempting to go beyond the Hubble classification has increased largely. Why, despite of this, the Hubble classification and its sequence are still alive and no alternative have yet emerged (Sandage, 2005)? My feeling is that the results of the multivariate analyses are not easily integrated into a one-century old practice of modeling the observations. In addition, extragalactic objects like galaxies, stellar clusters or stars do evolve. Astronomy now provides data on very distant objects, raising the question of the relationships between those and our present day nearby galaxies. Clearly, this is a phylogenetic problem. Astrocladistics 1 aims at exploring the use of phylogenetic tools in astrophysics (Fraix-Burnet et al., 2006a,b). We have proved that Maximum Parsimony (or cladistics) can be applied in astrophysics and provides a new exploration tool of the data (Fraix-Burnet et al., 2009, 2012, Cardone \& Fraix-Burnet, 2013). As far as the classification of galaxies is concerned, a larger number of objects must now be analysed. In this paper, IComment: Proceedings of the 60th World Statistics Congress of the International Statistical Institute, ISI2015, Jul 2015, Rio de Janeiro, Brazi

PHYLOGENETIC RELATIONSHIPS AMONG WEST INDIAN XENODONTINE SNAKES (SERPENTES; COLUBRIDAE) WITH COMMENTS ON THE PHYLOGENY OF SOME MAINLAND XENODONTINES

The evolutionary relationships of the West Indian (W. I.) xenodontine snake assemblage has been considered as either monophyletic or paraphyletic. Allozyme data from protein electrophoresis were used to estimate the phylogeny of the W. I. xenodontine snakes. Forty-two species from 25 genera (mainland and W. I. taxa) were examined. The phylogenetic relationships were estimated using parsimony analyses with successive approximation weighting on the data coded two ways: (1) the allele as the character and (2) the locus as the character. The most parsimonious trees from both coding methods indicated a non-monophyletic W. I. xenodontine assemblage. Three W.I. groups were recovered in both coding methods: (1) Jamaican Arrhyton and Darlingtonia, (2) Uromacer and the Cuban Arrhyton, and (3) Alsophis, Ialtris, and the South American Alsophis elegans. The relationships of Hypsirhynchus, Antillophis and Arrhyton exiguum were unstable. Nomenclatural changes are recommended for Darlingtonia, Arrhyton, Ialtris and Alsophis

W(h)ither Fossils? Studying Morphological Character Evolution in the Age of Molecular Sequences

A major challenge in the post-genomics era will be to integrate molecular sequence data from extant organisms with morphological data from fossil and extant taxa into a single, coherent picture of phylogenetic relationships; only then will these phylogenetic hypotheses be effectively applied to the study of morphological character evolution. At least two analytical approaches to solving this problem have been utilized: (1) simultaneous analysis of molecular sequence and morphological data with fossil taxa included as terminals in the analysis, and (2) the molecular scaffold approach, in which morphological data are analyzed over a molecular backbone (with constraints that force extant taxa into positions suggested by sequence data). The perceived obstacles to including fossil taxa directly in simultaneous analyses of morphological and molecular sequence data with extant taxa include: (1) that fossil taxa are missing the molecular sequence portion of the character data; (2) that morphological characters might be misleading due to convergence; and (3) character weighting, specifically how and whether to weight characters in the morphological partition relative to characters in the molecular sequence data partition. The molecular scaffold has been put forward as a potential solution to at least some of these problems. Using examples of simultaneous analyses from the literature, as well as new analyses of previously published morphological and molecular sequence data matrices for extant and fossil Chiroptera (bats), we argue that the simultaneous analysis approach is superior to the molecular scaffold approach, specifically addressing the problems to which the molecular scaffold has been suggested as a solution. Finally, the application of phylogenetic hypotheses including fossil taxa (whatever their derivation) to the study of morphological character evolution is discussed, with special emphasis on scenarios in which fossil taxa are likely to be most enlightening: (1) in determining the sequence of character evolution; (2) in determining the timing of character evolution; and (3) in making inferences about the presence or absence of characteristics in fossil taxa that may not be directly observable in the fossil record. Published By: Missouri Botanical Garde