Phylogenetics of extant and fossil Pinaceae: methods for increasing topological stability

Abstract

Abstract:Relationships of living and fossil Pinaceae were inferred using parsimony and Bayesian inference of morphological characters and plastid and nuclear DNA sequences. When considering extant taxa only, adding molecular to morphological characters resulted in markedly increased resolution and branch support compared with analysis of morphology alone. Including 45 fossil taxa resulted in drastically decreased resolution in morphology-based consensus trees. We evaluated the effect on branch support and resolution of including DNA sequences, deleting fossils lacking information for cone scale apices and seeds, using reduced consensus methods, and using implied weighting, and found that the greatest improvements were found by including DNA sequences and using implied weighting. The tree topologies from parsimony and Bayesian inference confirm previous findings that the fossil genus Pseudoaraucaria and a few species of Pityostrobus from the Lower Cretaceous are related to abietoid genera, and that other species of Pityostrobus are pinoid and closely related to Pinus. Focusing phylogenetic analyses on the most complete fossil cones, specifically those that are anatomically preserved and include both cone scale apices and seeds, and taking into account homoplasy, resulted in the clearest hypotheses for the timing and sequence of diversification in the family.Key words: fossil, morphology, phylogenetics, Pinaceae, PHYP.Résumé : Les relations qui existent entre les Pinaceae vivants et fossiles ont été déduites par la parcimonie et l'inférence Bayésienne des traits morphologiques et des séquences d'ADN plastidique et nucléaire. En considérant les taxons encore existants seulement, l'ajout de traits moléculaires aux traits morphologiques résultait en un accroissement marqué de la résolution et du support des branches comparativement à l'analyse de la morphologie seule. L'inclusion de 45 taxons fossiles résultait en une résolution fortement diminuée dans les arbres consensuels basés sur la morphologie. Les auteurs ont évalué l'effet d'inclure les séquences d'ADN sur le support des branches et la résolution, en supprimant les fossiles pour lesquels l'information sur les apex des écailles des cônes et des graines était manquante, en utilisant des méthodes de consensus réduites, et en utilisant une pondération implicite, et ils ont trouvé que les plus grandes améliorations étaient obtenues en incluant les séquences d'ADN et en utilisant la pondération implicite. Les topologies des arbres à partir de la parcimonie et de l'inférence Bayési-enne confirment les résultats précédents voulant que les fossiles du genre Pseudoaraucaria et quelques espèces de Pityostrobus du Crétacée inférieur soient apparentés au genre abiétoïde et que les autres espèces de Pityostrobus soient pinoïdes et étroitement apparentées aux Pinus. En concentrant les analyses phylogénétiques sur les cônes fossiles les plus complets, spécifiquement ceux qui sont anatomiquement préservés et qui comprennent les apex des écailles des cônes et les graines, et e...

Incorporating fossils into the Pinaceae tree of life

“…We expanded a data set from a previous study from 23 to 31 extant Pinaceae terminals (Gernandt et al., ; Appendix S2). Five genera were represented by multiple extant species: Abies (four), Larix (two), Pseudotsuga (two), Picea (four), and Pinus (13).…”

“…The outgroup sampling remained unchanged from Gernandt et al. (). We included one extant species from each of the other five extant conifer families and Ginkgo biloba (Ginkgoaceae).…”

“…Among other extant families, the fossil records of Cupressaceae and Sciadopityaceae may extend to the Triassic (Yao et al., ; Stockey et al., ), Araucariaceae to the Early Jurassic (Rothwell et al., ; Escapa and Catalano, ), and Podocarpaceae to the Triassic (Townrow, ; Rothwell et al., ). It is uncertain whether E. mackenziei diverged before or after the most recent common ancestor of all extant Pinaceae (Gernandt et al., ), but its discovery shows that the basic features of pinaceous ovulate cones had evolved by that time. These characters include bract‐scale complexes that are helically arranged and free from each other distally, resin canals present in the axis, scale and bract tissues, and two inverted seeds per scale, each with an adaxially attached wing.…”

“…Most molecular phylogenetic studies of Pinaceae have recovered a pinoid clade ( Cathaya , Larix , Picea , Pinus , and Pseudotsuga ) and either an abietoid clade or grade ( Abies , Cedrus , Keteleeria , Nothotsuga , Pseudolarix , and Tsuga ; Price et al., ; Wang et al., ; Gernandt et al., , ). These two groups were recognized based on root and shoot anatomy (van Tieghem, ; Chamberlain, ) and seed cone and seed morphology (Frankis, ).…”

“…An important result of previous attempts to analyze living taxa together with fossil seed cones is the instability of the inferred topologies (Smith and Stockey, , ; Pol and Escapa, ; Gernandt et al., , ). This instability has been attributed to the inclusion of fossils, which have many morphological character states coded as missing and lack information for molecular characters.…”