scholarly journals Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

2016 ◽  
Vol 12 (4) ◽  
pp. 20150975 ◽  
Author(s):  
Joseph E. O'Reilly ◽  
Philip C. J. Donoghue
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Molecular Clocks ◽  
Fossil Species ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Accuracy And Precision ◽  
Age Constraints ◽  
Age Estimates

Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone.

scholarly journals A fossil species of the enigmatic early polypod fern genus Cystodium (Cystodiaceae) in Cretaceous amber from Myanmar

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Ledis Regalado ◽  
Alexander R. Schmidt ◽  
Marc S. Appelhans ◽  
Bork Ilsemann ◽  
Harald Schneider ◽  
...  
Keyword(s):  
Solomon Islands ◽  
Divergence Time ◽  
Fossil Species ◽  
Burmese Amber ◽  
Divergence Time Estimates ◽  
Tropical Plant ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Fertile Leaf ◽  
Minimum Age

Abstract The monospecific fern genus Cystodium (Cystodiaceae; Polypodiales) occurs exclusively in the tropical forests of the Malay Archipelago, the Admiralty Islands, the Louisiade Archipelago, and the Solomon Islands. Divergence time estimates suggest that the genus originated in the Mesozoic; however, fossil evidence to validate this suggestion has been lacking. Amber from Myanmar (Burmese amber) is an important source of new information on the diversity of vascular cryptogams in the Cretaceous. This paper describes the fossil taxon Cystodium sorbifolioides nov. sp. based on a fragment of a fertile leaf preserved in Burmese amber that represents the first fossil evidence of the family Cystodiaceae. Cystodium sorbifolioides is used to obtain a minimum age estimate for the Cystodiaceae and the closely related, monogeneric Lonchitidaceae and Lindsaeaceae. The fossil strengthens the hypothesis that the forest ecosystems of Malesia and Melanesia represent refugia for many tropical plant lineages that originated in the Cretaceous.

scholarly journals Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

scholarly journals Problems related to the taxonomic placement of incompletely preserved amber fossils: transfer of the Paleogene liverwort <i>Cylindrocolea dimorpha</i> (Cephaloziellaceae) to the extant <i>Odontoschisma</i> sect. <i>Iwatsukia</i> (Cephaloziaceae)

Fossil Record ◽  
2017 ◽  
Vol 20 (2) ◽  
pp. 147-157 ◽  
Author(s):  
Kathrin Feldberg ◽  
Jiří Váňa ◽  
Alfons Schäfer-Verwimp ◽  
Michael Krings ◽  
Carsten Gröhn ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Divergence Time ◽  
New Combination ◽  
Crown Group ◽  
Fossil Species ◽  
Dna Sequence Data ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
The Baltic

Abstract. A revision of the Baltic and Bitterfeld amber fossils assigned to Cylindrocolea dimorpha (Cephaloziellaceae) has yielded evidence of the presence of multicellular, bifid underleaves, which have not previously been reported for this species and conflict with the current circumscription of the family. We transfer the fossil species to Odontoschisma (sect. Iwatsukia) and propose the new combination O. dimorpha of the Cephaloziaceae. Characteristics of the fossil include an overall small size of the plant, entire-margined, bifid leaves and underleaves, more or less equally thickened leaf cell walls, ventral branching that includes stoloniform branches with reduced leaves, and the lack of a stem hyalodermis and gemmae. Placement of the fossil in Cephaloziaceae profoundly affects divergence time estimates for liverworts based on DNA sequence variation with integrated information from the fossil record. Our reclassification concurs with hypotheses on the divergence times of Cephaloziaceae derived from DNA sequence data that provide evidence of a late Early Cretaceous to early Eocene age of the Odontoschisma crown group and an origin of O. sect. Iwatsukia in the Late Cretaceous to Oligocene.

scholarly journals A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

Fossil Record ◽  
2017 ◽  
Vol 20 (2) ◽  
pp. 201-213 ◽  
Author(s):  
Julia Bechteler ◽  
Alexander R. Schmidt ◽  
Matthew A. M. Renner ◽  
Bo Wang ◽  
Oscar Alejandro Pérez-Escobar ◽  
...  
Keyword(s):  
Divergence Time ◽  
Character State ◽  
Posterior Density ◽  
Crown Group ◽  
Burmese Amber ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Leafy Liverwort ◽  
Highest Posterior Density ◽  
Age Estimates

Abstract. DNA-based divergence time estimates suggested major changes in the composition of epiphyte lineages of liverworts during the Cretaceous; however, evidence from the fossil record is scarce. We present the first Cretaceous fossil of the predominantly epiphytic leafy liverwort genus Radula in ca. 100 Myr old Burmese amber. The fossil's exquisite preservation allows first insights into the morphology of early crown group representatives of Radula occurring in gymnosperm-dominated forests. Ancestral character state reconstruction aligns the fossil with the crown group of Radula subg. Odontoradula; however, corresponding divergence time estimates using the software BEAST lead to unrealistically old age estimates. Alternatively, assignment of the fossil to the stem of subg. Odontoradula results in a stem age estimate of Radula of 227.8 Ma (95 % highest posterior density (HPD): 165.7–306.7) and a crown group estimate of 176.3 Ma (135.1–227.4), in agreement with analyses employing standard substitution rates (stem age 235.6 Ma (142.9–368.5), crown group age 183.8 Ma (109.9–289.1)). The fossil likely belongs to the stem lineage of Radula subg. Odontoradula. The fossil's modern morphology suggests that switches from gymnosperm to angiosperm phorophytes occurred without changes in plant body plans in epiphytic liverworts. The fossil provides evidence for striking morphological homoplasy in time. Even conservative node assignments of the fossil support older rather than younger age estimates of the Radula crown group, involving origins for most extant subgenera by the end of the Cretaceous and diversification of their crown groups in the Cenozoic.

scholarly journals Fossil Constraints on the Timescale of Parasitic Helminth Evolution

2020 ◽  
Author(s):  
Kenneth De Baets ◽  
Paula Dentzien-Dias ◽  
G. William M. Harrison ◽  
D. Timothy J. Littlewood ◽  
Luke A. Parry
Keyword(s):  
Fossil Record ◽  
Divergence Time ◽  
Late Paleozoic ◽  
Early Paleozoic ◽  
Parasitic Helminths ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Molecular Divergence ◽  
Animal Hosts

The fossil record of parasitic helminths is often stated to be severely limited. Many studies have therefore used host constraints to constrain molecular divergence time estimates of helminths. Here we review direct fossil evidence for several of these parasitic lineages belong to various phyla (Acanthocephala, Annelida, Arthropoda, Nematoda, Nematomorpha, Pentastomida, Platyhelminthes). Our compilation shows that the fossil record of soft-bodied helminths is patchy, but more diverse than commonly assumed. The fossil record provides evidence that ectoparasitic helminths (e.g., worm-like pentastomid arthropods) have been around since the early Paleozoic, while endoparasitic helminths (cestodes) arose at least during, or possibly even before the late Paleozoic. Nematode lineages parasitizing terrestrial plant and animal hosts have been in existence at least since the Devonian and Triassic, respectively. All major phyla (Acanthocephala, Annelida, Platyhelminthes. Nematoda, Nematomorpha) had evolved endoparasitic lineages at least since the Mesozoic. Interestingly, although parasitism is considered derived within Metazoa, the oldest evidence for Nematoda and Platyhelminthes includes body fossils of parasitic representatives. Furthermore, the oldest fossil evidence of these parasitic lineages often falls within molecular divergence time estimates based on host co-evolution suggesting the fossil record of helminths themselves might be just as good or at least complementary (and less circular in justification) to calibration based on host associations. Data also provide evidence for obvious host switches or extinctions, which cautions against models of pure co-divergence where use of host calibrations to constrain divergence time estimates may be considered.

scholarly journals The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates

Palaeontology ◽  
2019 ◽  
Vol 63 (1) ◽  
pp. 67-83 ◽  
Author(s):  
Hans P. Püschel ◽  
Joseph E. O'Reilly ◽  
Davide Pisani ◽  
Philip C. J. Donoghue
Keyword(s):  
Divergence Time ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Accuracy And Precision ◽  
Stratigraphic Ranges ◽  
The Impact

scholarly journals Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal

2015 ◽  
Vol 11 (7) ◽  
pp. 20150321 ◽  
Author(s):  
Björn Stelbrink ◽  
Alena A. Shirokaya ◽  
Catharina Clewing ◽  
Tatiana Y. Sitnikova ◽  
Larisa A. Prozorova ◽  
...  
Keyword(s):  
Lake Baikal ◽  
Hydrothermal Vents ◽  
Divergence Time ◽  
Nuclear Data ◽  
Species Flock ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Younger Age ◽  
Abyssal Zone ◽  
Age Estimates

Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake Baikal limpet radiation, and to date the beginning of intra-lacustrine diversification. Divergence time estimates suggest a considerably younger age for the species flock compared with lake age estimates, and the beginning of extensive diversification is possibly related to rapid deepening and cooling during rifting. Phylogenetic relationships and divergence time estimates do not clearly indicate when exactly the abyssal was colonized but suggest a timeframe coincident with the formation of the abyssal in the northern basin (Middle to Late Pleistocene).

scholarly journals Multiple morphological clocks and total-evidence tip-dating in mammals

2016 ◽  
Vol 12 (7) ◽  
pp. 20160033 ◽  
Author(s):  
Michael S. Y. Lee
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Morphological Integration ◽  
Total Evidence ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Divergence Dates ◽  
Correlated Characters

Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or ‘pacemaker’. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.

Estimating divergence times of notothenioid fishes using a fossil-calibrated molecular clock

2004 ◽  
Vol 16 (1) ◽  
pp. 37-44 ◽  
Author(s):  
THOMAS J. NEAR
Keyword(s):  
Maximum Likelihood ◽  
Molecular Clock ◽  
Nucleotide Substitution ◽  
Divergence Time ◽  
Divergence Times ◽  
Substitution Rates ◽  
Cold Adapted ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Nucleotide Substitution Rates

Hypotheses concerning the diversification of notothenioid fishes have relied extensively on estimates of divergence times using molecular clock methods. The timing of diversification of the cold adapted antifreeze glycoprotein (AFGP)-bearing Antarctic notothenioid clade in the middle to late Miocene has been correlated with the onset of polar climatic conditions along the Antarctic Continental Shelf. Critical examination of the previous molecular clock analyses of notothenioids reveals several problems associated with heterogeneity of nucleotide substitution rates among lineages, the application of potentially inappropriate nucleotide substitution rates, and the lack of confidence intervals for divergence time estimates. In this study, the notothenioid partial gene mtDNA 12S-16S rRNA (PG-rRNA) molecular clock was reanalysed using a tree-based maximum likelihood strategy that attempts to account for rate heterogeneity of nucleotide substitution rates among lineages using the penalized likelihood method, and bootstrap resampling to estimate confidence intervals of divergence time estimates. The molecular clock was calibrated using the notothenioid fossil Proeleginops grandeastmanorum. Divergence time estimates for all nodes in the PG-rRNA maximum likelihood tree were substantially older than previous estimates. In particular, the estimated age of the AFGP-bearing Antarctic notothenioid clade predates the onset of extensive sea ice and development of polar conditions by at least 10 million years. Despite caveats involving the fossil calibration and limitations of the PG-rRNA dataset, these divergence time estimates provide initial observations for the development of a novel model of the diversification of cold adapted Antarctic notothenioid fishes.

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