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.

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 Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

2017 ◽  
Author(s):  
Mario dos Reis ◽  
Gregg F. Gunnell ◽  
José Barba-Montoya ◽  
Alex Wilkins ◽  
Ziheng Yang ◽  
...  
Keyword(s):  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Test Case ◽  
Base Pairs ◽  
Molecular Sequence Data ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Clock Models

AbstractPrimates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

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 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 Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

2020 ◽  
Author(s):  
Alexandre Hassanin ◽  
Géraldine Véron ◽  
Anne Ropiquet ◽  
Bettine Jansen van Vuuren ◽  
Alexis Lécu ◽  
...  
Keyword(s):  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Early Eocene Climatic Optimum ◽  
Time Estimates ◽  
History Of ◽  
Nucleotide Divergence ◽  
Final Alignment ◽  
Complete Mitochondrial Genomes

AbstractThe order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 22 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

scholarly journals Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0240770
Author(s):  
Alexandre Hassanin ◽  
Géraldine Veron ◽  
Anne Ropiquet ◽  
Bettine Jansen van Vuuren ◽  
Alexis Lécu ◽  
...  
Keyword(s):  
Divergence Time ◽  
Mitochondrial Genomes ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Early Eocene Climatic Optimum ◽  
Time Estimates ◽  
History Of ◽  
Nucleotide Divergence ◽  
Final Alignment ◽  
Complete Mitochondrial Genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil calibration points to estimate a molecular timescale for carnivorans. According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.

scholarly journals A posteriori evaluation of molecular divergence dates using empirical estimates of time-heterogeneous fossilization rates

2017 ◽  
Author(s):  
Simon Gunkel ◽  
Jes Rust ◽  
Torsten Wappler ◽  
Christoph Mayer ◽  
Oliver Niehuis ◽  
...  
Keyword(s):  
Fossil Record ◽  
Divergence Time ◽  
Simulated Data ◽  
Divergence Times ◽  
Data Sets ◽  
A Posteriori ◽  
Divergence Time Estimates ◽  
Empirical Estimates ◽  
Time Estimates ◽  
Log Normal

AbstractThe application of molecular clock concepts in phylogenetics permits estimating the divergence times of clades with an incomplete fossil record. However, the reliability of this approach is disputed, because the resulting estimates are often inconsistent with different sets of fossils and other parameters (clock models and prior settings) in the analyses. Here, we present the λ statistic, a likelihood approach for a posteriori evaluating the reliability of estimated divergence times. The λ statistic is based on empirically derived fossilization rates and evaluates the fit of estimated divergence times to the fossil record. We tested the performance of this measure with simulated data sets. Furthermore, we applied it to the estimated divergence times of (i) Clavigeritae beetles of the family Staphylinidae and (ii) all extant insect orders. The reanalyzed beetle data supports the originally published results, but shows that several fossil calibrations used do not increase the reliability of the divergence time estimates. Analyses of estimated inter-ordinal insect divergences indicate that uniform priors with soft bounds marginally outperform log-normal priors on node ages. Furthermore, a posteriori evaluation of the original published analysis indicates that several inter-ordinal divergence estimates might be too young. The λ statistic allows the comparative evaluation of any clade divergence estimate derived from different calibration approaches. Consequently, the application of different algorithms, software tools, and calibration schemes can be empirically assessed.

Molecular relationships of the cuscuses, brushtail and scaly-tailed possums (Phalangerinae)

2002 ◽  
Vol 50 (2) ◽  
pp. 135 ◽  
Author(s):  
M. J. Osborne ◽  
L. Christidis
Keyword(s):  
Middle Miocene ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Species Relationships ◽  
Base Pairs ◽  
Dna Sequence Data ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Relationships

DNA sequence data (1040 base pairs) from the mitochondrial nicotinamide dehydrogenase subunit 2 gene (ND2) was used to elucidate species relationships within the Phalangerinae (cuscuses, brushtail and scaly-tailed possums). Phylogenetic analyses revealed three lineages within this family (Spilocuscus, Phalanger and Trichosurus-Wyulda), which is congruent with the results of other molecular studies. Sequence data also demonstrate that P. orientalis, P. carmelitae, P. vestitus, and P. sericeus are closely related and indicates that P. gymnotis is the sister lineage to the genus Phalanger. Divergence time estimates indicate that the radiation of Phalanger and Spilocuscus occurred during the middle Miocene to Pliocene periods.

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