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 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 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 Amblyomma birmitum a new species of hard tick in Burmese amber

Parasitology ◽  
2017 ◽  
Vol 144 (11) ◽  
pp. 1441-1448 ◽  
Author(s):  
LIDIA CHITIMIA-DOBLER ◽  
BRUNO CANCIAN DE ARAUJO ◽  
BERNHARD RUTHENSTEINER ◽  
TIMO PFEFFER ◽  
JASON A. DUNLOP
Keyword(s):  
New Record ◽  
Divergence Time ◽  
Hard Tick ◽  
Burmese Amber ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Gondwana Supercontinent ◽  
Tick Genus ◽  
Radiation Time ◽  
A New Species

SUMMARYAmblyomma birmitum sp. nov. is formally described as a new record from 99 Ma old Burmese amber from Myanmar. This confirms the presence of the extant hard tick genus Amblyomma C.L. Koch, 1844 (Ixodida: Ixodidae) in the Late Cretaceous. This discovery is placed in its wider context and some reports of fossil hard ticks, such as a Hyalomma C.L. Koch, 1844 in Eocene Baltic amber, are misidentifications. The genus Amblyomma belongs to the clade Metastriata, a group which probably also accommodates two extinct genera, Cornupalpatum Poinar and Brown, 2003 and Compluriscutata Poinar and Buckley, 2008, also found in Burmese amber. All three fossils are thus only a little younger than published molecular divergence time estimates (ca. 124 ± 17 Ma) for the Metastriata lineage. Amblyomma has a largely Gondwanan distribution today. However, in some biogeographical scenarios, e.g. the Samafrica model, its predicted radiation time postdates the dissolution of the original Gondwana supercontinent raising questions about how its current distribution pattern was achieved.

Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽  
2009 ◽  
Vol 2107 (1) ◽  
pp. 41-52 ◽  
Author(s):  
CAROLINA M VOLOCH ◽  
PABLO R FREIRE ◽  
CLAUDIA A M RUSSO
Keyword(s):  
Fossil Record ◽  
Divergence Time ◽  
Penaeid Shrimp ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Global Clock ◽  
Late Tertiary ◽  
The Family ◽  
Molecular Studies ◽  
Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

scholarly journals Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

2012 ◽  
Vol 279 (1742) ◽  
pp. 3501-3509 ◽  
Author(s):  
Prashant P. Sharma ◽  
Gonzalo Giribet
Keyword(s):  
Late Cretaceous ◽  
Divergence Time ◽  
Disjunct Distribution ◽  
Continental Margins ◽  
Divergence Time Estimates ◽  
Evolutionary Origins ◽  
Source Regions ◽  
Time Estimates ◽  
Fiji Islands ◽  
The Pacific

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous ( ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

scholarly journals Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i884-i894
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Time Reversibility ◽  
Sequence Alignments ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Substitution Process ◽  
The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

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