Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

There exists a remarkable correlation between genetic distance and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies on extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here did not support these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils

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

A fossil byblidaceae seed from eocene South Australia

Copyright © 2004 by The University of ChicagoA single mummified angiosperm seed is described from a middle Eocene clay lens deposit at the Monier East Yatala Sand Pit, Golden Grove, South Australia. The seed is small (0.7 mm long and 0.45 mm wide), elliptical, black, and shows complex raised reticulate honeycomb sculpturing with deeply excavated cell floors and verrucate sculpturing on the anticlinal ridges. The fossil was compared against extant species of Byblis and the Droseraceae, especially the Drosera indica L. complex, common annual carnivorous plants that grow in seasonally damp environments in northern Australia and that have similarly small sculptured seeds. The combination of deep reticulately honeycombed cells and the verrucate anticlinal walls places the seed close to extant taxa in the Byblis liniflora Salisb. complex. However, in the absence of a larger sample and/or of definitive features to assign the fossil unequivocally to an extant species, as well as nomenclatural restrictions preventing the typification of a fossil by an illustration, the specimen is described as a parataxon and placed in Byblidaceae but without a formal name.Conran, John G., and David C. Christophe

Asymptotic genealogy of a critical branching process

Consider a continuous-time binary branching process conditioned to have population size n at some time t, and with a chance p for recording each extinct individual in the process. Within the family tree of this process, we consider the smallest subtree containing the genealogy of the extant individuals together with the genealogy of the recorded extinct individuals. We introduce a novel representation of such subtrees in terms of a point-process, and provide asymptotic results on the distribution of this point-process as the number of extant individuals increases. We motivate the study within the scope of a coherent analysis for an a priori model for macroevolution.Comment: 30 page

Jörg Wunderlich (ed.) (2012): Fifteen papers on extant and fossil spiders (Araneae)

This book consists of fifteen papers (considered below as Chapters) on fossil and extant arachnids, mostly spiders. Most papers are written by the editor, two papers in cooperation with Peter Jäger and with Søren Toft, and a single one by Peter Jäger. Chapters 1 and 2 are identification keys to the European genera of the families Zodariidae and Corinnidae, respectively

Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201