Timetrees: Incorporating Fossils and Molecules

Editorial

30 June 2022

Editorial: Timetrees: Incorporating fossils and molecules

Michel Laurin

Gilles Didier

and

Rachel C. M. Warnock

1,529 views

0 citations

Editors

Michel Laurin

UMR7207 Centre de recherche sur la paléobiodiversité et les paléoenvironnements (CR2P)

Gilles Didier

UMR5149 Institut Montpelliérain Alexander Grothendieck (IMAG)

Rachel C M Warnock

ETH Zürich

Impact

Average timetree resulting from application of the calibrations described here (mostly in the Supplementary Material). As in Table 2 and in Irisarri et al. (2017: figure 3), the bars on the nodes are the superimposed 95% credibility intervals from the two runs in PhyloBayes. The calibrations are shown as red arrows horizontally in line with the nodes they apply to; note that the arrow that is almost aligned with the branch of Lalagobatrachia and the one that is almost aligned with the terminal branch for Silurana are the maximum and minimum ages of Node 178 (Pipidae), the one on Iguana to Node 131 (Iguania), and the one on Pelodiscus to Node 117 (Testudines). The abbreviated genus names are spelled out as clade names on their common branches; where only one species per genus is sampled, see Irisarri et al. (2017) for full species names. To the extent possible, clade names with minimum-clade (node-based) definitions are placed close to those nodes, while names with maximum-clade (branch-based) definitions are shown close to the origin of that branch (i.e., the preceding node if sampled) and undefined names stay in the middle. Period/epoch symbols from oldest to youngest: Cambrian (cut off at 500 Ma), Ordovician, Silurian, Devonian, Carboniferous, Permian, Triassic, Jurassic, Early Cretaceous, Late Cretaceous, Paleogene, and Neogene including Quaternary (which comprises the last 2.58 Ma and is not shown separately). Timescale (including colors) from the International Chronostratigraphic Chart, version 2020/03 (Cohen K. M. et al., 2020). Node numbers, also used in the text and the tables, are from Irisarri et al. (2017).

Hypothesis and Theory

12 May 2021

The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

David Marjanović

Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.

15,006 views

11 citations

Selected fossils representing node-age calibrations. (A) Tulerpeton curtum, after Lebedev and Coates (1995); (B) Horton Bluff colosteid-like taxon; (C) Horton Bluff embolomere-like taxon; (D) Lethiscus stocki, segmented skull based on micro-CT; (E) type specimen of Balanerpeton woodi, after Milner and Sequeira (1993); (F) Gerobatrachus hottoni; (G) Triadobatrachus massinoti; (H) type specimen of Hylonomus lyelli.

Review

16 October 2020

Can We Reliably Calibrate Deep Nodes in the Tetrapod Tree? Case Studies in Deep Tetrapod Divergences

Jason D. Pardo

, 1 more and

Jason S. Anderson

7,426 views

16 citations

Monotreme placement. Kishino–Hasegawa tests (in IQ-TREE) for the alternative placements of Australosphenida on (A) the NCDP mammal backbone constraint phylogeny for the mandibulodental, cranial, and postcranial data for (B) the full character set and (C) excluding cheek teeth and shoulder girdle characters. The placement of Australosphenida is rejected in red (P < 0.05), not rejected in green (P > 0.1), and weakly rejected when not highlighted (P = 0.05–0.1). Placement 8 corresponds to the placement of Australosphenida within or adjacent to eutriconodonts and is inclusive of placements 7 and 8, and any placements with Jeholodens or Yanoconodon.

Original Research

08 July 2020

Conflict Resolution for Mesozoic Mammals: Reconciling Phylogenetic Incongruence Among Anatomical Regions

Mélina A. Celik

and

Matthew J. Phillips

5,933 views

13 citations

Brachiopod MCC trees obtained using the FBD analysis with interval ages, median ages and random ages, and unconstrained analysis. Posterior support is shown for each node for all trees. Error bars on the FBD trees show the 95% HPD interval for the age of each node, as well as the age of each fossil in the tree with interval ages.

Original Research

26 June 2020

Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference

Joëlle Barido-Sottani

, 4 more and

Rachel C. M. Warnock

5,968 views

41 citations

Uncorrelated clock models produce stronger deviations from the strict clock constraint in larger trees. y-axis: variance of the tip-to-root distances. x-axis: number of tips. Deviation from the strict molecular clock hypothesis was generated using the uncorrelated exponential model. The scatterplot derives from the analysis of 20,000 observations, each observation being a value for the tip-to-root variance and the corresponding number of tips.

Hypothesis and Theory

27 May 2020

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

Stéphane Guindon

5,616 views

21 citations

Brief Research Report

11 March 2020

A Cambrian–Ordovician Terrestrialization of Arachnids

Jesus Lozano-Fernandez

, 4 more and

Davide Pisani

Chelicerate divergence times in the molecular clock analysis (outgroups not shown). Divergence times shown are obtained under the CIR autocorrelated, relaxed molecular clock model. Nodes in the tree represent average divergence times. The density plots represent the posterior distributions from the considered node. The numbered blue circles represent the age of the fossil calibrations and are located at a height corresponding to the node they are calibrating (see Table 1). In the timescale on the X axis, numbers represent millions of years before the present.

Understanding the temporal context of terrestrialization in chelicerates depends on whether terrestrial groups, the traditional Arachnida, have a single origin and whether or not horseshoe crabs are primitively or secondarily marine. Molecular dating on a phylogenomic tree that recovers arachnid monophyly, constrained by 27 rigorously vetted fossil calibrations, estimates that Arachnida originated during the Cambrian or Ordovician. After the common ancestor colonized the land, the main lineages appear to have rapidly radiated in the Cambrian–Ordovician boundary interval, coinciding with high rates of molecular evolution. The highest rates of arachnid diversification are detected between the Permian and Early Cretaceous. A pattern of ancient divergence estimates for terrestrial arthropod groups in the Cambrian while the oldest fossils are Silurian (seen in both myriapods and arachnids) is mirrored in the molecular and fossil records of land plants. We suggest the discrepancy between molecular and fossil evidence for terrestrialization is likely driven by the extreme sparseness of terrestrial sediments in the rock record before the late Silurian.

14,880 views

51 citations

Comparison of average slopes for each of the seven scenarios in the four callibration setting. Gradient of color represents the accuracy of the estimates yellow is ± 5%, Orange ± 10% red = ± 15%. Each data point represents the average slope of the 10 concatensions of true time vs. estimate time with ±1 standard deviation.

Original Research

20 March 2020

Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment

Christopher Lowell Edward Powell

, 1 more and

Fabia Ursula Battistuzzi

4,277 views

23 citations

Original Research

17 January 2020

A Total Evidence Phylogenetic Analysis of Pinniped Phylogeny and the Possibility of Parallel Evolution Within a Monophyletic Framework

Ryan S. Paterson

, 2 more and

Hillary C. Maddin

In the present study, a series of phylogenetic analyses of morphological, molecular, and combined morphological-molecular datasets were conducted to investigate the relationships of 23 extant and 44 fossil caniforme genera, in order to test the phylogenetic position of putative stem pinniped Puijila within a comprehensive evolutionary framework. With Canis as an outgroup, a Bayesian Inference analysis employing tip-dating of a combined molecular-morphological (i.e., Total Evidence) dataset recovered a topology in which musteloids are the sister group to a monophyletic pinniped clade, to the exclusion of ursids, and recovered Puijila and Potamotherium along the stem of Pinnipedia. A similar topology was recovered in a parsimony analysis of the same dataset. These results suggest the pinniped stem may be expanded to include additional fossil arctoid taxa, including Puijila, Potamotherium, and Kolponomos. The tip-dating analysis suggested a divergence time between pinnipeds and musteloids of ~45.16 million years ago (Ma), though a basal split between otarioids and phocids is not estimated to occur until ~26.52 Ma. These results provide further support for prolonged freshwater and nearshore phases in the evolution of pinnipeds, prior to the evolution of the extreme level of aquatic adaptation displayed by extant taxa. Ancestral character state reconstruction was used to investigate character evolution, to determine the frequency of reversals and parallelisms characterizing the three extant clades within Pinnipedia. Although the phylogenetic analyses did not directly provide any evidence of parallel evolution within the pinniped extant families, it is apparent from the inspection of previously-proposed pinniped synapomorphies, within the context of a molecular-based phylogenetic framework, that many traits shared between extant pinnipeds have arisen independently in the three clades. Notably, those traits relating to homodonty and limb-bone specialization for aquatic locomotion appear to have multiple origins within the crown group, as suggested by the retention of the plesiomorphic conditions in early-diverging fossil members of the three extant families. Thus, while the present analysis identifies a new suite of morphological synapomorphies for Pinnipedia, the frequency of reversals and other homoplasies within the clade limit their diagnostic value.

18,979 views

43 citations

Systematic Review

29 November 2019

Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary

Mark S. Springer

, 3 more and

William J. Murphy

, 2013). Analyses were performed with a molecular scaffold that was based on robustly supported clades (>95% bootstrap support) from Meredith et al.’s (2011) phylogenetic analysis of 26 nuclear loci. The molecular scaffold included several polytomies that are not yet confidently resolved by molecular data: trichotomy at root of Placentalia (Afrotheria, Boreoeutheria, Xenarthra), paenungulate trichotomy (Hyracoidea, Proboscidea, Sirenia), Euarchontoglires trichotomy (Primatomorpha, Glires, Scandentia), and Laurasiatheria polytomy (Carnivora+Pholidota, Chiroptera, Cetartiodactyla, Perissodactyla). Pseudoextinct taxa were made pseudoextinct by recoding soft tissue characters as missing and deleting the pseudoextinct taxon from the molecular scaffold. Maximum parsimony analyses of 19 ordinal level taxa were individually executed with PAUP 4.0a165 (Swofford, 2002) and compared to the master scaffold. Parsimony analyses for each pseudoextinct clade were performed with 1000 random input orders of taxa and tree-bisection and reconnection branch swapping. Mammalian orders that showed shifts in phylogenetic position in these analyses are indicated by arrows that show the movements of entire clades as well as the repositioning of subtaxa within or among orders. Only four orders (Lagomorpha, Hyracoidea, Proboscidea, Sirenia) did not show changes to phylogenetic relationships in these analyses. Monotreme outgroups were included in the original analysis but were pruned from the tree shown here. Paintings are by C. Buell.

Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.

16,964 views

49 citations

Review

12 November 2019

Using the Fossil Record to Evaluate Timetree Timescales

Charles R. Marshall

The fossil and geologic records provide the primary data used to established absolute timescales for timetrees. For the paleontological evaluation of proposed timetree timescales, and for node-based methods for constructing timetrees, the fossil record is used to bracket divergence times. Minimum brackets (minimum ages) can be established robustly using well-dated fossils that can be reliably assigned to lineages based on positive morphological evidence. Maximum brackets are much harder to establish, largely because it is difficult to establish definitive evidence that the absence of a taxon in the fossil record is real and not just due to the incompleteness of the fossil and rock records. Five primary methods have been developed to estimate maximum age brackets, each of which is discussed. The fact that the fossilization potential of a group typically decreases the closer one approaches its time of origin increases the challenge of estimating maximum age brackets. Additional complications arise: 1) because fossil data actually bracket the time of origin of the first relevant fossilizable morphology (apomorphy), not the divergence time itself; 2) due to the phylogenetic uncertainty in the placement of fossils; 3) because of idiosyncratic temporal and geographic gaps in the rock and fossil records; and 4) if the preservation potential of a group changed significantly during its history. In contrast, uncertainties in the absolute ages of fossils are typically relatively unimportant, even though the vast majority of fossil cannot be dated directly. These issues and relevant quantitative methods are reviewed, and their relative magnitudes assessed, which typically correlate with the age of the group, its geographic range, and species richness.

12,474 views

63 citations