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.

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 Uncertainty in divergence time estimation

2020 ◽  
Author(s):  
Tom Carruthers ◽  
Robert W Scotland
Keyword(s):  
Fossil Record ◽  
Academic Research ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation ◽  
Diversification Rates ◽  
Divergence Time Estimates ◽  
Use Of Time ◽  
Time Estimates ◽  
Highly Sensitive

Abstract Understanding and representing uncertainty is crucial in academic research, because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogenies are interpreted. With respect to methods, we discuss how the assumptions underlying different methods may not adequately reflect uncertainty about molecular evolution, the fossil record, or diversification rates. Therefore, divergence time estimates may not adequately reflect uncertainty, and may be directly contradicted by subsequent findings. For the interpretation of time-calibrated phylogenies, we discuss how the use of time-calibrated phylogenies for reconstructing general evolutionary timescales leads to inferences about macroevolution that are highly sensitive to methodological limitations in how uncertainty is accounted for. By contrast, we discuss how the use of time-calibrated phylogenies to test specific hypotheses leads to inferences about macroevolution that are less sensitive to methodological limitations. Given that many biologists wish to use time-calibrated phylogenies to reconstruct general evolutionary timescales, we conclude that the development of methods of divergence time estimation that adequately account for uncertainty is necessary.

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 Bees diversified in the age of eudicots

2013 ◽  
Vol 280 (1755) ◽  
pp. 20122686 ◽  
Author(s):  
Sophie Cardinal ◽  
Bryan N. Danforth
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Close Association ◽  
Divergence Time ◽  
Dominant Group ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Time Calibration ◽  
Angiosperm Species ◽  
Almost All

Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113–132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.

scholarly journals Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

2012 ◽  
Vol 279 (1742) ◽  
pp. 3491-3500 ◽  
Author(s):  
Mario dos Reis ◽  
Jun Inoue ◽  
Masami Hasegawa ◽  
Robert J. Asher ◽  
Philip C. J. Donoghue ◽  
...  
Keyword(s):  
Fossil Record ◽  
Bayesian Method ◽  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Limited Data ◽  
Base Pairs ◽  
Rapid Radiation ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Dating Methods

The fossil record suggests a rapid radiation of placental mammals following the Cretaceous–Paleogene (K–Pg) mass extinction 65 million years ago (Ma); nevertheless, molecular time estimates, while highly variable, are generally much older. Early molecular studies suffer from inadequate dating methods, reliance on the molecular clock, and simplistic and over-confident interpretations of the fossil record. More recent studies have used Bayesian dating methods that circumvent those issues, but the use of limited data has led to large estimation uncertainties, precluding a decisive conclusion on the timing of mammalian diversifications. Here we use a powerful Bayesian method to analyse 36 nuclear genomes and 274 mitochondrial genomes (20.6 million base pairs), combined with robust but flexible fossil calibrations. Our posterior time estimates suggest that marsupials diverged from eutherians 168–178 Ma, and crown Marsupialia diverged 64–84 Ma. Placentalia diverged 88–90 Ma, and present-day placental orders (except Primates and Xenarthra) originated in a ∼20 Myr window (45–65 Ma) after the K–Pg extinction. Therefore we reject a pre K–Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach.

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.

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