Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Time Estimates ◽

Early Diversification ◽

Extant Species ◽

Tree Inference ◽

Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been instrumental to resolving the suprafamilial backbone of the charadriiform tree, several higher-level relationships, including the monophyly of plovers (Charadriidae) and the phylogenetic positions of several monotypic families, have remained unclear. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 336 ingroup taxa (89\% of all extant species), 24 loci (15 mitochondrial and 9 nuclear), and 69 morphological characters. Using this phylogeny, we clarify the charadriiform evolutionary timeline by conducting a node-dating analysis based on a subset of 8 loci tested to be clock-like and 16 carefully selected, updated, and vetted fossil calibrations. Our concatenated, species-tree, and total-evidence analyses consistently support plover monophyly and are generally congruent with the topologies of previous studies, suggesting that the higher-level relationships among shorebirds are largely settled. However, several localized conflicts highlight areas of persistent uncertainty within the gulls (Laridae), true auks (Alcinae), and sandpipers (Scolopacidae). At shallower levels, our phylogenies reveal instances of genus-level nonmonophyly that suggest changes to currently accepted taxonomies. Our node-dating analyses consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades. However, age estimates for more recent divergences vary between different relaxed clock models, and we demonstrate that this variation can affect phylogeny-based macroevolutionary studies. Our findings demonstrate the impact of fossil calibration choice on the resulting divergence time estimates, and the sensitivity of diversification rate analyses to the modeling assumptions made in time tree inference.

Closing the gap between rocks and clocks using total-evidence dating

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0136 ◽

2016 ◽

Vol 371 (1699) ◽

pp. 20150136 ◽

Cited By ~ 48

Author(s):

Fredrik Ronquist ◽

Nicolas Lartillot ◽

Matthew J. Phillips

Keyword(s):

Sampling Rate ◽

Divergence Time ◽

Branch Length ◽

Morphological Characters ◽

Total Evidence ◽

Background Information ◽

Time Estimates ◽

Wide Range ◽

Correlated Characters

Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push divergence events back in time when using inadequate models or vague priors, a phenomenon we term ‘deep root attraction’ (DRA). We identify several causes of DRA. Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques. Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid diversification, rare extinction or high fossil sampling rate; any of these assumptions produces highly congruent divergence time estimates with a minimal gap between rocks and clocks. Under these conditions, fossils have a stabilizing influence on divergence time estimates and significantly increase the precision of those estimates, which are generally close to the dates suggested by palaeontologists. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

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

Bioinformatics ◽

10.1093/bioinformatics/btaa820 ◽

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 ◽

Time Estimates ◽

Substitution Process ◽

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.

Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

The Canadian Entomologist ◽

10.4039/tce.2021.42 ◽

2021 ◽

pp. 1-28

Author(s):

Yoshimasa Kumekawa ◽

Haruka Fujimoto ◽

Osamu Miura ◽

Ryo Arakawa ◽

Jun Yokoyama ◽

...

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Ryukyu Archipelago ◽

Time Estimates ◽

Molecular Phylogenetic ◽

History Of ◽

Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

Ignoring Fossil Age Uncertainty Leads to Inaccurate Topology and Divergence Time Estimates in Time Calibrated Tree Inference

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2020.00183 ◽

2020 ◽

Vol 8 ◽

Cited By ~ 2

Author(s):

Joëlle Barido-Sottani ◽

Nina M. A. van Tiel ◽

Melanie J. Hopkins ◽

David F. Wright ◽

Tanja Stadler ◽

...

Keyword(s):

Divergence Time ◽

Time Estimates ◽

Tree Inference

Exploring the impact of fossil constraints on the divergence time estimates of derived liverworts

Plant Systematics and Evolution ◽

10.1007/s00606-012-0745-y ◽

2013 ◽

Vol 299 (3) ◽

pp. 585-601 ◽

Cited By ~ 22

Author(s):

Kathrin Feldberg ◽

Jochen Heinrichs ◽

Alexander R. Schmidt ◽

Jiří Váňa ◽

Harald Schneider

Keyword(s):

Divergence Time ◽

Time Estimates ◽

The Implications of Lineage-Specific Rates for Divergence Time Estimation

Systematic Biology ◽

10.1093/sysbio/syz080 ◽

2019 ◽

Vol 69 (4) ◽

pp. 660-670 ◽

Cited By ~ 1

Author(s):

Tom Carruthers ◽

Michael J Sanderson ◽

Robert W Scotland

Keyword(s):

Estimation Error ◽

Divergence Time ◽

Time Estimation ◽

Rate Variation ◽

Data Set ◽

Divergence Time Estimation ◽

Time Estimates ◽

The Impact ◽

Highest Posterior Density

Abstract Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.]

Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies

Systematic Biology ◽

10.1093/sysbio/syz032 ◽

2019 ◽

Vol 69 (1) ◽

pp. 1-16 ◽

Cited By ~ 6

Author(s):

Yuan Nie ◽

Charles S P Foster ◽

Tianqi Zhu ◽

Ru Yao ◽

David A Duchêne ◽

...

Keyword(s):

Global Climate ◽

Divergence Time ◽

Tree Topology ◽

Molecular Dating ◽

Crown Group ◽

Green Plants ◽

Fossil Calibration ◽

Time Estimates ◽

Chloroplast Genomes

Abstract Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth’s climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.

Appropriate Assignment of Fossil Calibration Information Minimizes the Difference between Phylogenetic and Pedigree Mutation Rates in Humans

Life ◽

10.3390/life8040049 ◽

2018 ◽

Vol 8 (4) ◽

pp. 49 ◽

Cited By ~ 1

Author(s):

Renata Capellão ◽

Elisa Costa-Paiva ◽

Carlos Schrago

Keyword(s):

Mutation Rate ◽

Divergence Time ◽

Mutation Rates ◽

Human Populations ◽

Fossil Calibration ◽

Time Estimates ◽

The Mean ◽

The Difference ◽

Coalescent Time

Studies that measured mutation rates in human populations using pedigrees have reported values that differ significantly from rates estimated from the phylogenetic comparison of humans and chimpanzees. Consequently, exchanges between mutation rate values across different timescales lead to conflicting divergence time estimates. It has been argued that this variation of mutation rate estimates across hominoid evolution is in part caused by incorrect assignment of calibration information to the mean coalescent time among loci, instead of the true genetic isolation (speciation) time between humans and chimpanzees. In this study, we investigated the feasibility of estimating the human pedigree mutation rate using phylogenetic data from the genomes of great apes. We found that, when calibration information was correctly assigned to the human–chimpanzee speciation time (and not to the coalescent time), estimates of phylogenetic mutation rates were statistically equivalent to the estimates previously reported using studies of human pedigrees. We conclude that, within the range of biologically realistic ancestral generation times, part of the difference between whole-genome phylogenetic and pedigree mutation rates is due to inappropriate assignment of fossil calibration information to the mean coalescent time instead of the speciation time. Although our results focus on the human–chimpanzee divergence, our findings are general, and relevant to the inference of the timescale of the tree of life.

Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae)

10.1101/2020.09.03.280941 ◽

2020 ◽

Author(s):

Sebastián Escobar ◽

Andrew J. Helmstetter ◽

Rommel Montúfar ◽

Thomas L. P. Couvreur ◽

Henrik Balslev

Keyword(s):

Phylogenetic Relationships ◽

Divergence Time ◽

Historical Biogeography ◽

Time Estimates ◽

Early Diversification ◽

Time Calibration ◽

Vegetable Ivory ◽

Andean Uplift ◽

Magdalena River

AbstractThe vegetable ivory palms (Phytelepheae) form a small group of Neotropical palms whose phylogenetic relationships are not fully understood. Three genera and eight species are currently recognized; however, it has been suggested that Phytelephas macrocarpa could include the species Phytelephas seemannii and Phytelephas schottii because of supposed phylogenetic relatedness and similar morphology. We inferred their phylogenetic relationships and divergence time estimates using the 32 most clock-like loci of a custom palm bait-kit formed by 176 genes and four fossils for time calibration. We additionally explored the historical biogeography of the tribe under the recovered phylogenetic relationships. Our fossil-dated tree showed the eight species previously recognized, and that P. macrocarpa is not closely related to P. seemanii and P. schottii, which, as a consequence, should not be included in P. macrocarpa. The ancestor of the vegetable ivory palms was widely-distributed in the Chocó, the inter-Andean valley of the Magdalena River, and the Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma can be attributed to trans-Andean vicariance between the Chocó/Magdalena and the Amazonia. Our results support the role of Andean uplift in the early diversification of Phytelephas under new phylogenetic relationships inferred from genomic data.

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

10.1101/2020.07.09.195487 ◽

2020 ◽

Author(s):

Jose Barba-Montoya ◽

Qiqing Tao ◽

Sudhir Kumar

Keyword(s):

Divergence Time ◽

Sequence Divergence ◽

Molecular Dating ◽

Divergence Times ◽

Time Reversibility ◽

Sequence Alignments ◽

Time Estimates ◽

Substitution Process ◽

AbstractMotivationAs 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.ResultsWe 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.AvailabilityAll datasets are deposited in Figshare: https://doi.org/10.6084/[email protected]