Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

O'Connor, Anne; Wills, Matthew A.

doi:10.1093/sysbio/syw039

Cited by 21 publications

(16 citation statements)

References 147 publications

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“…Many studies contrast the stratigraphic gaps implicit to inferred phylogenies from different taxa or intervals of time (e.g., Benton and Storrs 1994; Hitchin and Benton 1997; Wills 1999, 2007; Benton et al 2000; O'Connor et al 2011). O'Connor and Wills (2016) assess a variety of reasons why differences might exist other than sampling, although they do not include differences in diversification rates. Bapst (2013) shows that differences in diversification offer another reason why two clades with otherwise similar preservation potential will have phylogenies with different summed branch durations and thus stratigraphic gaps.…”

Section: Discussionmentioning

confidence: 99%

On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification and sampling vary over time

Wagner¹

2019

Paleobiology

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The time separating the first appearances of species from their divergences from related taxa affects assessments of macroevolutionary hypotheses about rates of anatomical or ecological change. Branch durations necessarily posit stratigraphic gaps in sampling within a clade over which we have failed to sample predecessors (ancestors) and over which there are no divergences leading to sampled relatives (sister taxa). The former reflects only sampling rates, whereas the latter reflects sampling, origination, and extinction rates. Because all three rates vary over time, the probability of a branch duration of any particular length will differ depending on when in the Phanerozoic that branch duration spans. Here, I present a birth–death-sampling model allowing interval-to-interval variation in diversification and sampling rates. Increasing either origination or sampling rates increases the probability of finding sister taxa that diverge both during and before intervals of high sampling/origination. Conversely, elevated extinction reduces the probability of divergences from sampled sister taxa before and during intervals of elevated extinction. In the case of total extinction, a Signor-Lipps will reduce expected sister taxa leading up to the extinction, with the possible effect stretching back many millions of years when sampling is low. Simulations indicate that this approach provides reasonable estimates of branch duration probabilities under a variety of circumstances. Because current probability models for describing morphological evolution are less advanced than methods for inferring diversification and sampling rates, branch duration priors allowing for time-varying diversification could be a potent tool for phylogenetic inference with fossil data.

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Section: Discussionmentioning

confidence: 99%

On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification and sampling vary over time

Wagner¹

2019

Paleobiology

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“…These sites are critically important for the arthropod fossil record because of their relatively low preservation potential of many groups, as is particularly the case for terrestrial arthropods, being less well mineralised than many of the marine groups. This is reflected in the low level of congruence between the order of appearance of lineages in the fossil record (stratigraphic appearance) and the order of phylogenetic branching (Wills, 2001;O'Connor and Wills, 2016) in arthropods, as compared to more congruent datasets such as tetrapods (Benton et al, 1999(Benton et al, , 2000Norell and Novacek, 1992). Clustering of calibrations at Konservat-Lagerstätten localities may lead to highly variable lengths of ghost lineages for the different taxa that are preserved together at these sites, and indeed many of the clades in our database have soft maxima that are substantially older than their hard minimum date.…”

Section: Discussionmentioning

confidence: 99%

Fossil Calibrations for the Arthropod Tree of Life

Wolfe

Daley

Legg³

et al. 2016

Preprint

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Fossil age data and molecular sequences are increasingly combined to establish a timescale for the Tree of Life. Arthropods, as the most species-rich and morphologically disparate animal phylum, have received substantial attention, particularly with regard to questions such as the timing of habitat shifts (e.g., terrestrialisation), genome evolution (e.g., gene family duplication and functional evolution), origins of novel characters and behaviours (e.g., wings and flight, venom, silk), biogeography, rate of diversification (e.g., Cambrian explosion, insect coevolution with angiosperms, evolution of crab body plans), and the evolution of arthropod microbiomes. We present herein a series of rigorously vetted calibration fossils for arthropod evolutionary history, taking into account recently published guidelines for best practice in fossil calibration. These are restricted to Palaeozoic and Mesozoic fossils, no deeper than ordinal taxonomic level, nonetheless resulting in 79 fossil calibrations for 101 clades. This work is especially timely owing to the rapid growth of molecular sequence data and the fact that many included fossils have been described within the last five years. This contribution provides a resource for systematists and other biologists interested in deep-time questions in arthropod evolution.

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“…The high SCI and GER values of cynodonts contrast with their low MSM* values (22%). It has been observed that tetrapods in general have a lower MSM* (<50%) than plants, fishes or echinoderms, but higher than arthropods and molluscs (O'Connor & Wills 2016). MSM* has been found to be heavily biased by tree size and shape (Siddall 1998), more so than SCI and GER, and it does not correlate strongly with other metrics (O'Connor & Wills 2016).…”

Section: Discussionmentioning

confidence: 99%

“…It has been observed that tetrapods in general have a lower MSM* (<50%) than plants, fishes or echinoderms, but higher than arthropods and molluscs (O'Connor & Wills 2016). MSM* has been found to be heavily biased by tree size and shape (Siddall 1998), more so than SCI and GER, and it does not correlate strongly with other metrics (O'Connor & Wills 2016). Furthermore, MSM* is negatively correlated with the number of taxa included within the tree (O'Connor & Wills 2016), which might explain why the value for cynodonts is low given the relatively high number of taxa used here.…”

Section: Discussionmentioning

confidence: 99%

Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

2021

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Mammals are the only surviving group of Cynodontia, a synapsid clade that first appeared in the fossil record in the late Permian, ~260 million years ago. Using three metrics that capture skeletal completeness, we quantify the quality of the early cynodont fossil record in time and space to evaluate the impact of sampling and preservational biases on our understanding of the group's evolutionary history. There is no consistent global sampling signal for early cynodonts. Completeness of the cynodont fossil record increases across the Permian–Triassic boundary, peaking in the Early to early Late Triassic. This peak is dominated by specimens from southern Africa and South America, where a highly seasonal climate probably favoured preservation. Completeness is generally lower thereafter, correlating with a shift from a Gondwanan to a predominantly Laurasian fossil record. Phylogenetic and stratigraphic congruence in early cynodonts is high, although their fossil record exhibits less skeletal completeness overall than other tetrapod clades, including the contemporaneous anomodont synapsids. This discrepancy could be due to differences in the diagnosability of their fossils, especially for small‐bodied species. Establishing the timing and assembly of derived (‘mammalian’) anatomical features in Cynodontia is obscured by sampling. Two of the major nodes at which acquisition of mammalian features is concentrated (Cynodontia and Mammaliamorpha) suffer from lengthy intervals of poor sampling before becoming abundant parts of tetrapod faunas. Low completeness in these intervals limits our ability to determine when certain ‘key’ mammalian characteristics evolved, or to identify the selective pressures that might have driven their origins.

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Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

Cited by 21 publications

References 147 publications

On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification and sampling vary over time

On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification and sampling vary over time

Fossil Calibrations for the Arthropod Tree of Life

Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

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