Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved--"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv--to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence dates were generally greater than ages inferred from ND dating; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We favour the FBD-derived ages because they best match the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099--0.0549) and 0.0240 (0.0039--0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling, therefore these estimates should be treated with caution.

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Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

10.1101/2020.09.25.313643 ◽

2020 ◽

Author(s):

Michael R. May ◽

Dori L. Contreras ◽

Michael A. Sundue ◽

Nathalie S. Nagalingum ◽

Cindy V. Looy ◽

...

Keyword(s):

Morphological Evolution ◽

Divergence Time ◽

Time Estimation ◽

Bayes Factors ◽

Total Evidence ◽

Rate Variation ◽

Divergence Time Estimation ◽

Extinction Rates ◽

Extant Species ◽

Tree Models

AbstractPhylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or “tip-dating”) approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data, and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization), and thus provide a coherent and biologically interpretable tree prior. To explore the behaviour of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the Middle Devonian and Upper Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ∼2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades are made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification.

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Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2005.3124 ◽

2005 ◽

Vol 272 (1572) ◽

pp. 1577-1586 ◽

Cited By ~ 180

Author(s):

Niklas Wahlberg ◽

Michael F Braby ◽

Andrew V.Z Brower ◽

Rienk de Jong ◽

Ming-Min Lee ◽

...

Keyword(s):

Dna Sequences ◽

Synergistic Effects ◽

Strong Support ◽

Sister Group ◽

Morphological Characters ◽

Molecular Data ◽

Total Evidence ◽

Data Matrix ◽

Morphological Data ◽

Combined Analysis

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions ( COI , EF-1α and wingless ). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1α data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.

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A phylogenetic approach to the Philippines endemic centipedes of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae), with the description of a new species

Zootaxa ◽

10.11646/zootaxa.4483.3.1 ◽

2018 ◽

Vol 4483 (3) ◽

pp. 401

Author(s):

CARLES DOMÉNECH ◽

VICTOR M. BARBERA ◽

EDUARDO LARRIBA

Keyword(s):

Dna Sequences ◽

Endemic Species ◽

Phylogenetic Trees ◽

Morphological Characters ◽

Genetic Distances ◽

The Philippines ◽

Neighbor Joining ◽

Separate Species ◽

Additional Species ◽

A New Species

The genus Scolopendra Linnaeus, 1758 is represented in the Philippines’ fauna by five species, two of which are endemic. Mitochondrial DNA sequences of gene cytochrome c oxidase subunit I (COI) were obtained from six Scolopendra specimens belonging to two endemic species and a new one, described here as Scolopendra paradoxa Doménech sp. nov. These sequences were analyzed together with another forty-one sequences from GenBank, including additional species of Scolopendra and a few representatives of other Scolopendridae genera. Phylogenetic trees inferred from the COI analysis using maximum likelihood and neighbor joining showed the three Philippines Scolopendra endemic species as a polyphyletic group coherent with their respective morphologies, although the position of S. spinosissima Kraepelin, 1903 varied within the obtained trees. Species delimitation based on standard external morphological characters was also concordant with the observed genetic distances, monophyly and node support, confirming S. subcrustalis Kronmüller, 2009 and S. paradoxa sp. nov. as separate species also at the molecular level, while only the position of S. spinosissima could not be properly established with any of the statistical methods used. In addition, the male genitalia of the three studied species were found to lack gonopods and a penis. Remarks on the ultimate legs prefemoral spinous formula of S. spinosissima plus a key to the species of the genus Scolopendra in the Philippines are provided.

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Arthropod Origins: Integrating Paleontological and Molecular Evidence

Annual Review of Ecology Evolution and Systematics ◽

10.1146/annurev-ecolsys-011720-124437 ◽

2020 ◽

Vol 51 (1) ◽

pp. 1-25

Author(s):

Gregory D. Edgecombe

Keyword(s):

Nervous System ◽

Fossil Record ◽

Morphological Characters ◽

Molecular Data ◽

Trace Fossils ◽

Total Evidence ◽

Molecular Evidence ◽

Stem Group ◽

Clock Analysis ◽

Coherent Picture

Phylogenomics underpins a stable and mostly well-resolved hypothesis for the interrelationships of extant arthropods. Exceptionally preserved fossils are integrated into this framework by coding their morphological characters, as exemplified by total-evidence dating approaches that treat fossils as dated tips in analyses numerically dominated by molecular data. Cambrian fossils inform on the sequence of character acquisition in the arthropod stem group and in the stems of its main extant clades. The arthropod head problem incorporates unique appendage combinations and remains of the nervous system in fossils into a scheme mostly based on neuroanatomy and Hox expression domains for extant forms. Molecular estimates of arthropod origins in the Cryogenian or Ediacaran predate a coherent picture from the arthropod fossil record, which commences as trace fossils in the earliest Cambrian. Probabilistic morphological clock analysis of trilobites, which exemplify the earliest arthropod body fossils, supports a Cambrian origin, without the need to posit an unfossilized Ediacaran history.

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A molecular perspective on the evolution of scleractinian corals

The Paleontological Society Papers ◽

10.1017/s1089332600000048 ◽

1996 ◽

Vol 1 ◽

pp. 39-57 ◽

Cited By ~ 3

Author(s):

Sandra L. Romano

Keyword(s):

Dna Sequences ◽

Fossil Record ◽

Nuclear Dna ◽

Genome Structure ◽

Divergence Time ◽

Morphological Diversity ◽

Morphological Characters ◽

Molecular Data ◽

Scleractinian Corals ◽

Molecular Techniques

The evolutionary history of scleractinian corals, based on morphological taxonomy and inferences from the fossil record, has been poorly understood. Molecular techniques developed over the past ten years are now being used to gain a new perspective on scleractinian phylogeny. DNA sequences, mitochondrial genome structure, and morphological characters support a basal position for the Anthozoa in the phylum Cnidaria. Mitochondrial and nuclear DNA sequences suggest a relatively derived position of the order Scleractinia within the class Anthozoa. Mitochondrial and nuclear DNA sequences have provided a new hypothesis for evolution within the Scleractinia that is different from hypotheses based on morphological characters of extant and fossil taxa. Groupings within the two major lineages defined by molecular data do not correspond to morphological suborder groupings although groupings of genera within families do correspond to traditional taxonomy. This new molecular hypothesis suggests that the Scleractinia are represented by two major lineages that diverged from each other before the appearance of the scleractinian skeleton in the fossil record. This divergence time supports the hypotheses that the Scleractinia are not related to the Rugosa of the Paleozoic and that the scleractinian skeleton has evolved more than once. These two major lineages may represent two architectural strategies within the Scleractinia that have led to their great morphological diversity.

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Phylogenomics supports a Cenozoic rediversification of the “living fossil” Isoetes

10.1101/2019.12.23.886994 ◽

2019 ◽

Cited By ~ 1

Author(s):

Daniel Wood ◽

Guillaume Besnard ◽

David J. Beerling ◽

Colin P. Osborne ◽

Pascal-Antoine Christin

Keyword(s):

Fossil Record ◽

Molecular Dating ◽

Rate Variation ◽

Nuclear Markers ◽

Living Fossil ◽

Chloroplast Genomes ◽

Genome Wide ◽

Extant Species ◽

Dating Methods ◽

Insight Into

AbstractThe fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

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

10.1101/2021.07.15.452585 ◽

2021 ◽

Author(s):

David Černý ◽

Rossy Natale

Keyword(s):

Divergence Time ◽

Morphological Characters ◽

Total Evidence ◽

Fossil Calibration ◽

Divergence Time Estimates ◽

Time Estimates ◽

Early Diversification ◽

Extant Species ◽

Tree Inference ◽

The Impact

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.

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Phylogeny and divergence times of suckers (Cypriniformes: Catostomidae) inferred from Bayesian total-evidence analyses of molecules, morphology, and fossils

PeerJ ◽

10.7717/peerj.5168 ◽

2018 ◽

Vol 6 ◽

pp. e5168 ◽

Cited By ~ 3

Author(s):

Justin C. Bagley ◽

Richard L. Mayden ◽

Phillip M. Harris

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Fossil Record ◽

Total Evidence ◽

Morphological Data ◽

Divergence Times ◽

Data Types ◽

Multiple Data ◽

Phylogenetic Informativeness ◽

Divergence Dating

Catostomidae (“suckers”) is a diverse (76 species) and broadly distributed family of Holarctic freshwater fishes with a rich fossil record and a considerable number (∼35%) of threatened and imperiled species. We integrate DNA sequences (three mitochondrial genes, three nuclear genes), morphological data, and fossil information to infer sucker phylogenetic relationships and divergence times using Bayesian “total-evidence” methods, and then test hypotheses about the temporal diversification of the group. Our analyses resolved many nodes within subfamilies and clarified Catostominae relationships to be of the form ((Thoburniini, Moxostomatini), (Erimyzonini, Catostomini)). Patterns of subfamily relationships were incongruent, but mainly supported two placements of the Myxocyprininae; distinguishing these using Bayes factors lent strongest support to a model with Myxocyprininae sister to all remaining sucker lineages. We improved our Bayesian total-evidence dating analysis by excluding problematic characters, using a clock-partitioning scheme identified by Bayesian model selection, and employing a fossilized birth-death tree prior accommodating morphological data and fossils. The resulting chronogram showed that suckers evolved since the Late Cretaceous–Eocene, and that the Catostomini and Moxostomatini clades have accumulated species diversity since the early to mid-Miocene. These results agree with the fossil record and confirm previous hypotheses about dates for the origins of Catostomide and catostomine diversification, but reject previous molecular hypotheses about the timing of divergence of ictiobines, and between Asian–North American lineages. Overall, our findings from a synthesis of multiple data types enhance understanding of the phylogenetic relationships, taxonomic classification, and temporal diversification of suckers, while also highlighting practical methods for improving Bayesian divergence dating models by coupling phylogenetic informativeness profiling with relaxed-clock partitioning.

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The identification of the species of the ‘Spilogona contractifrons species-group’ and the ‘Spilogona nitidicauda species-group’ (Diptera, Muscidae) based on morphological and molecular analysis

European Journal of Taxonomy ◽

10.5852/ejt.2018.484 ◽

2018 ◽

Cited By ~ 1

Author(s):

Vera S. Sorokina ◽

Elena V. Shaikevich

Keyword(s):

Dna Sequences ◽

Morphological Characters ◽

Species Group ◽

Genetic Distances ◽

Valid Species ◽

Separate Species ◽

Cytochrome Oxidase I Gene ◽

Male Head ◽

Morphological Differences ◽

I Gene

Muscid species of the ‘Spilogona contractifrons species-group’ (Spilogona alticola (Malloch, 1920), S. arctica (Zetterstedt, 1838), S. contractifrons (Zetterstedt, 1838), S. orthosurstyla Xue & Tian, 1988) and of the ‘Spilogona nitidicauda species-group’ (S. nitidicauda (Schnabl, 1911), S. hissarensis Hennig, 1959, S. imitatrix (Malloch, 1921), S. platyfrons Sorokina, 2018) are notoriously difficult to distinguish. In this paper, their morphological features are analysed, images of the male head, frons and abdomen of all the species are given, and the male terminalia are figured. The study of extensive material has shown that all the morphologically recognised species in each of these groups are valid species. An identification key is provided for both groups of species. To confirm the morphological differences, genetic differences in the cytochrome oxidase I gene of flies of the ‘Spilogona contractifrons species-group’ and of the ‘Spilogona nitidicauda species-group’ were analysed. It is shown that members of both groups of species have not only distinguishing morphological characters but also fixed substitutions in the DNA sequences. Since a low interspecific polymorphism is known in the Muscidae Latreille, 1802, the revealed genetic distances confirm the existence of separate species or subspecies in each of the groups studied.

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A dynamic global equilibrium in carnivoran diversification over 20 million years

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.2312 ◽

2014 ◽

Vol 281 (1778) ◽

pp. 20132312 ◽

Cited By ~ 39

Author(s):

Lee Hsiang Liow ◽

John A. Finarelli

Keyword(s):

Fossil Record ◽

Biological Diversity ◽

Species Turnover ◽

Extinction Rates ◽

Open Questions ◽

Level Data ◽

Extant Species ◽

Global Equilibrium ◽

Living Organisms ◽

Two Peaks

The ecological and evolutionary processes leading to present-day biological diversity can be inferred by reconstructing the phylogeny of living organisms, and then modelling potential processes that could have produced this genealogy. A more direct approach is to estimate past processes from the fossil record. The Carnivora (Mammalia) has both substantial extant species richness and a rich fossil record. We compiled species-level data for over 10 000 fossil occurrences of nearly 1400 carnivoran species. Using this compilation, we estimated extinction, speciation and net diversification for carnivorans through the Neogene (22–2 Ma), while simultaneously modelling sampling probability. Our analyses show that caniforms (dogs, bears and relatives) have higher speciation and extinction rates than feliforms (cats, hyenas and relatives), but lower rates of net diversification. We also find that despite continual species turnover, net carnivoran diversification through the Neogene is surprisingly stable, suggesting a saturated adaptive zone, despite restructuring of the physical environment. This result is strikingly different from analyses of carnivoran diversification estimated from extant species alone. Two intervals show elevated diversification rates (13–12 Ma and 4–3 Ma), although the precise causal factors behind the two peaks in carnivoran diversification remain open questions.

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