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The female lead is the part of Helen Rodin, a tough lawyer and the daughter of the local district attorney.According to The Hollywood Reporter, the studio wants a “pedigreed yet non-A-list actress” for the role.We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies.The results suggest that primates originated around the Cretaceous–Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone.There are, however, 17 species of extinct lemurs that are subfossils dating from 400–20,000 years ago (Godfrey et al. Calibrations of lemur divergence times have used multiple primate and nonprimate outgroups (e.g., Yoder and Yang 2000; Horvath et al. Recently published ancient DNA has allowed some of the subfossils to be placed in the tree with greater precision (Kistler et al. To close the gap between neontology and paleontology, we focus on the strepsirrhine primates: Lemuriformes from Madagascar and Lorisiformes from Africa and Asia. It has proven difficult to resolve the lemur phylogeny using molecular data alone (Yoder 1994; Yoder and Yang 2000; Horvath et al. In this study, we infer near-complete phylogenies of extant and extinct lemurs and their closest relatives with combined morphological and molecular data sets. We conducted searches for the best partitioning scheme using likelihood statistics, as implemented in Partition Finder software (Lanfear et al. We first specified each codon of each locus and then used the search algorithm to find the partitioning scheme that maximized the fit of the data to the model while minimizing the number of parameters, using the Bayesian information criterion as well as the second-order Akaike information criterion as the measure of model fit. The best-fitting partitioning scheme for the full-concatenated data set was one that included two partitions, each with their own model of sequence evolution: 1) all nuclear genes, first and second codon positions of (SYM G; Supplementary Table S2 available on Dryad).
*Correspondence to be sent to: Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West & 79th Street, New York, NY 10024, USA; Email: [email protected] and neontological systematics seek to answer evolutionary questions with different data sets.Extinct taxa inform us about the mode of character evolution and transitional forms (Slater et al. 2015), the timing of species origin and disappearance (Foote 2000), and species distributions in deep time (Patzkowsky and Holland 2012). 2012a) and parameterize the branching process of the phylogeny based on speciation and extinction rates from the fossil record (Heath et al. The model assumptions differ between these two approaches and the effects of these assumptions on results are becoming clear (e.g., Zhang et al. The first method, known as “tip-dating” (hereafter TD), uses TE data sets to model the substitution rate of the molecular and morphological data partitions with extant and fossil tips in the phylogeny (Pyron 2011; Ronquist et al. The TD method assumes a uniform prior probability on the branching process, such that branching events occur anywhere along internodes according to the branch lengths inferred from the data (Ronquist et al. In contrast to the uniform branching assumption, process-based models such as a birth–death model are especially suitable when the study group has had nonzero extinction (Condamine et al. The fossilized birth–death process (hereafter FBD), implements a model with a branching process prior based on diversification dynamics (speciation and extinction rates) calibrated with the fossil record (Heath et al. The utility of fossil dating methods in systematics is evident from the recent surge in publications using them (e.g., Wood et al. 2015) but the efficacy and comparability of the methods have only recently been addressed (Beck and Lee 2014; Grimm et al. The systematics of fossil and extant primates have been approached from two perspectives: paleontologists with morphological data and extensive sampling of extinct taxa (e.g., Seiffert et al. 2014a), or limitations of external calibration techniques that cannot use all available fossil information (Pyron 2011). Even with the extensive primate fossil record, multiple fossils are often reduced to calibrations of a single node; for example, 35 fossil taxa were reduced to 14 node calibrations in Springer et al. Calibration of the crown primate node has been suggested to be 55–56 Ma (Wilkinson et al. 2015), despite the fact that multiple fossils which may represent the first crown primates are known from a range of ages (e.g., Ni et al. Taxa for which morphological data were available and collected in this study are depicted with crossbones, and taxa for which molecular data were available are depicted with a double helix.Unfortunately, biased preservation, incomplete specimens, and the lack of molecular data for comparison to extant species impedes the phylogenetic placement of fossils (Wiens and Morrill 2011; Sansom 2015). Combining morphological and molecular data sets, especially including fossils, can improve phylogenetic inference. Other fossils have not been informative at all because stem taxa cannot be assigned to a node for calibration. Sequences for each locus were aligned using amino acid translation alignment in MAFFT (Katoh et al. Alignments were verified and edited manually as necessary (Supplementary File S5 and Tree BASE submission # 17704 available on Dryad).Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life.Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available.
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