Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

Caldas, Ian V.; Schrago, Carlos G.

doi:10.1002/ece3.4921

Cited by 14 publications

(18 citation statements)

References 53 publications

(72 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Unlike the Explosive and Long Fuse Models , both of which are widely advocated in the literature, support for the Short Fuse Model is restricted to a relatively small number of studies. These include early molecular clock analyses (e.g., Kumar and Hedges, 1998), a supertree analysis (Bininda-Emonds et al, 2007), and more recently morphological clock studies (Puttick et al, 2016; Caldas and Schrago, 2019). The most explicit support for the Short Fuse Model comes from Bininda-Emonds et al (2007), who used a matrix representation with parsimony approach to build a supertree representing ∼99% of mammalian species-level diversity.…”

Section: Review and Comparison Of Modelsmentioning

confidence: 99%

“…These authors recommended that the results of such analyses be treated with caution. Caldas and Schrago (2019) compared the results of molecular and morphological clocks with internal node calibrations and found that the majority of estimated ages were older with the morphological clock than the molecular clock. However, Caldas and Schrago (2019) estimated interordinal ages based on the morphological clock are younger than Puttick et al (2016) estimated ages based on the morphological clock with tip dating.…”

Section: Node Dating and Beyondmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2019

View full text Add to dashboard Cite

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.

show abstract

Section: Review and Comparison Of Modelsmentioning

confidence: 99%

Section: Node Dating and Beyondmentioning

confidence: 99%

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

et al. 2019

View full text Add to dashboard Cite

show abstract

“…While some investigators have compared dates from morphological and molecular data, they have generally used multiple calibrations in their analyses [e.g., 1,5,8]. Overall, they found that both data sources resulted in comparable time estimates, except for some morphological estimates that were older than molecular, depending on the choice of calibration priors and data partitioning.…”

Section: Discussionmentioning

confidence: 99%

“…The difference between the time estimates obtained from molecules and morphology is possibly because morphological matrices generally consist only of characters that vary among terminals; thus, the rate of morphological change, which ultimately impacts divergence time estimation, may be biased. Furthermore, it is generally accepted that phenotypic diagnostic changes of lineages will accumulate after their complete genetic isolation [27] while genetic changes may start well before the speciation time [8,28,29]. Therefore, the relative pace of the morphological clock should be slower than the molecular clock and thereby morphological time estimates could become younger than molecular time estimates.…”

Section: Analyses Without Internal Calibrationsmentioning

confidence: 99%

“…There is a growing interest in using morphological data to infer species divergence times in systematics by using it itself in morphological clock analyses [e.g., [1][2][3][4][5][6][7][8] or by combining it with molecular data in total-evidence dating approaches [e.g., [9][10][11][12][13][14]. In some total-evidence dating, morphological characters from dated fossil species and extant species are analyzed along with molecular data under models of morphological character evolution [e.g., 15].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular and morphological clocks for estimating evolutionary divergence times

Barba-Montoya

Tao

Kumar

2020

Preprint

View full text Add to dashboard Cite

Background: Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference. Results: We systematically analyzed three empirical datasets from different species groups to test the concordance of dates of species divergence inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths, because of an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging, but some considerable discordance between time estimates from molecules and morphology may still occur because some deeper branches show large difference from two types of data. Conclusions: Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with a large number of taxa. Nevertheless, we highlight the importance of evaluating the concordance of time structure in morphological and molecular data before any dating analysis using combined datasets.

show abstract

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

Pozzi

Penna

2022

Evolutionary Anthropology

View full text Add to dashboard Cite

In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total‐evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever‐increasing availability of genomic‐level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.

show abstract

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

Cited by 14 publications

References 53 publications

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

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

Molecular and morphological clocks for estimating evolutionary divergence times

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

Contact Info

Product

Resources

About