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      Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

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      Systematic Biology

      Oxford University Press

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          Abstract

          The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence—however measured—also varied throughout the Phanerozoic, reflecting the taxonomic composition of our sample. Notably, periods containing a high proportion of arthropods had poorer congruence overall than those with higher proportions of tetrapods. [Fossil calibration; gap excess ratio; manhattan stratigraphic metric; molecular clocks; stratigraphic congruence.]

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          Most cited references 54

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          Tunicates and not cephalochordates are the closest living relatives of vertebrates.

          Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage. This view is mainly justified by overall morphological similarities and an apparently increased complexity in cephalochordates and vertebrates relative to tunicates. Despite their critical importance for understanding the origins of vertebrates, phylogenetic studies of chordate relationships have provided equivocal results. Taking advantage of the genome sequencing of the appendicularian Oikopleura dioica, we assembled a phylogenomic data set of 146 nuclear genes (33,800 unambiguously aligned amino acids) from 14 deuterostomes and 24 other slowly evolving species as an outgroup. Here we show that phylogenetic analyses of this data set provide compelling evidence that tunicates, and not cephalochordates, represent the closest living relatives of vertebrates. Chordate monophyly remains uncertain because cephalochordates, albeit with a non-significant statistical support, surprisingly grouped with echinoderms, a hypothesis that needs to be tested with additional data. This new phylogenetic scheme prompts a reappraisal of both morphological and palaeontological data and has important implications for the interpretation of developmental and genomic studies in which tunicates and cephalochordates are used as model animals.
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            A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

            Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.]
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              Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs.

              The rise and diversification of the dinosaurs in the Late Triassic, from 230 to 200 million years ago, is a classic example of an evolutionary radiation with supposed competitive replacement. A comparison of evolutionary rates and morphological disparity of basal dinosaurs and their chief "competitors," the crurotarsan archosaurs, shows that dinosaurs exhibited lower disparity and an indistinguishable rate of character evolution. The radiation of Triassic archosaurs as a whole is characterized by declining evolutionary rates and increasing disparity, suggesting a decoupling of character evolution from body plan variety. The results strongly suggest that historical contingency, rather than prolonged competition or general "superiority," was the primary factor in the rise of dinosaurs.
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                Author and article information

                Journal
                Syst Biol
                Syst. Biol
                sysbio
                sysbio
                Systematic Biology
                Oxford University Press
                1063-5157
                1076-836X
                September 2016
                06 May 2016
                06 May 2016
                : 65
                : 5
                : 792-811
                Affiliations
                Milner Centre for Evolution, The University of Bath, The Avenue, Claverton Down, Bath BA2 7AY, UK
                Author notes
                *Correspondence to be sent to: The Milner Centre for Evolution, Department of Biology and Biochemistry, The University of Bath, The Avenue, Claverton Down, Bath BA2 7AY, UK; E-mail: m.a.wills@ 123456bath.ac.uk .

                Associate Editor: Peter Foster

                Article
                syw039
                10.1093/sysbio/syw039
                4997008
                27155010
                © The Author(s) 2016. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Pages: 20
                Categories
                Regular Articles

                Animal science & Zoology

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