Concept drift over geological times: predictive modeling baselines for analyzing the mammalian fossil record

PremiseThe ecological conditions that constrain plants to an environmental niche are assumed to be constant through time. While the fossil record has been used previously to test for niche conservatism of woody flowering plants, additional studies are needed in other plant groups especially since they can provide insight with paleoclimatic reconstructions, high biodiversity in modern terrestrial ecosystems, and significant contributions to agriculture.MethodsWe tested climatic niche conservatism across time by characterizing the climatic niches of living herbaceous ginger plants (Zingiberaceae) and woody dawn redwood (Metasequoia) against paleoniches reconstructed based on fossil distribution data and paleoclimatic models.ResultsDespite few fossil Zingiberaceae occurrences in the latitudinal tropics, unlike living Zingiberaceae, extinct Zingiberaceae likely experienced paratropical conditions in the higher latitudes, especially in the Cretaceous and Paleogene. The living and fossil distributions of Metasequoia largely remain in the upper latitudes of the northern hemisphere. The Zingiberaceae shifted from an initial subtropical climatic paleoniche in the Cretaceous, toward a temperate regime in the late Cenozoic; Metasequoia occupied a more consistent climatic niche over the same time intervals.ConclusionsBecause of the inconsistent climatic niches of Zingiberaceae over geologic time, we are less confident of using them for taxonomic‐based paleoclimatic reconstruction methods like nearest living relative, which assume a consistent climatic niche between extant and extinct relatives; we argue that the consistent climatic niche of Metasequoia is more appropriate for these reconstructions. Niche conservatism cannot be assumed between extant and extinct plants and should be tested further in groups used for paleoclimatic reconstructions.

Despite increasing concerns about the effect of sampling biases on our reading of the fossil record, few studies have considered the completeness of the fossil remains themselves, and those that have tend to apply non-quantitative measures of preservation quality. Here we outline two new types of metric for quantifying the completeness of the fossil remains of taxa through time, using sauropodomorph dinosaurs as a case study. The “Skeletal Completeness Metric” divides the skeleton up into percentages based on the amount of bone for each region, whereas the “Character Completeness Metric” is based on the number of characters that can be scored for each skeletal element in phylogenetic analyses. For both metrics we calculated the completeness of the most complete individual and of the type specimen. We also calculated how well the taxon as a whole is known from its remains. We then plotted these results against both geological and historical time, and compared curves of the former with fluctuations in sauropodomorph diversity, sea level, and sedimentary rock outcrop area. Completeness through the Mesozoic shows a number of peaks and troughs; the Early Jurassic (Hettangian–Sinemurian) is the interval with highest completeness, whereas the mid-to-Late Cretaceous has completeness levels that are consistently lower than the rest of the Mesozoic. Completeness shows no relationship to rock outcrop area, but it is negatively correlated with sea level during the Jurassic–Early Cretaceous and correlated with diversity in the Cretaceous. Completeness of sauropodomorph type specimens has improved from 1830 to the present, supporting the conclusions of other recent studies. However, when this time interval is partitioned, we find no trend for an increase in completeness from the 1990s onward. Moreover, the 2000s represent one of the poorest decades in terms of average type specimen completeness. These results highlight the need for quantitative methods when assessing fossil record quality through geological time or when drawing conclusions about historical trends in the completeness of taxa. The new metrics may also prove useful as sampling proxies in diversity studies.

ABSTRACTWe revisited questions about changes in the incidences of functional wood anatomical traits through geologic time and compared the incidences of these traits in the fossil record with modern wood anatomical diversity patterns in order to test classical (“Baileyan”) and more recent ecophyletic hypotheses of xylem evolution. We contrast patterns through time for tropical and higher (paleo)latitudes. Data are from the InsideWood database. There are striking differences between woods from high and mid latitudes versus tropical (paleo)-latitudes. At temperate and subtropical latitudes (Laurasia and high latitude Gondwana), the epoch by epoch time series supports the Baileyan transformation series of vessel-bearing woody angiosperms (basal woody angiosperms and eudicots): “primitive” features such as scalariform perforations, exclusively solitary vessels, apotracheal diffuse parenchyma and heterocellular rays abound in the Cretaceous and become much less frequent in the Cenozoic, especially post-Eocene. In contrast, in the paleotropics hardly any changes occur in the incidences – each epoch has an equally “modern” spectrum of wood anatomical attributes. Although climatic gradients from the poles to the equator were less steep in the Cretaceous than in the late Cenozoic, the wood anatomical differences between mid-high latitude woods and tropical woods were much more pronounced in the Cretaceous than in later epochs. This seeming paradox is discussed but we cannot resolve it.We suggest that tropical conditions have accelerated xylem evolution towards greater hydraulic efficiency (simple perforations), biological defense and hydraulic repair (elaborate paratracheal parenchyma patterns) as evidenced by late Cretaceous tropical latitude woods having near modern incidences of almost all traits. At higher paleolatitudes of both the Northern and Southern Hemisphere “ancestral” features such as scalariform perforations were retained in cooler and frost-prone regions where they were not selected against in mesic habitats because of lower demands on conductive efficiency, and could even be advantageous in trapping freeze-thaw embolisms. The fossil wood record remains too incomplete for testing hypotheses on the wood anatomy of the earliest angiosperms. The low incidence of so-called “xerophobic” woods sensu Feild with scalariform perforations with numerous (over 40) closely spaced bars in the Cretaceous tropical fossil record is puzzling. At higher paleolatitudes such woods are common in the Cretaceous.Ring porosity, an indicator of seasonal climates and deciduousness, occurs at low levels in the Cretaceous and Paleogene at higher paleolatitudes only, and reaches modern levels in the Miocene. In Neogene and Recent temperate Northern Hemisphere, wide vessels are virtually restricted to ring-porous woods. In the tropics, there is a low incidence of ring porosity throughout all epochs.The fossil record indicates that ecophysiological adaptation to tropical or temperate conditions was already evident in the Cretaceous with considerable latitudinal differences.

Willis, K.J., McElwain, J.C. The evolution of plants

Response to Comment by Faurby, Werdelin and Svenning

Estimating deep-time species-level diversification processes remains challenging. Both the fossil record and molecular phylogenies allow the estimation of speciation and extinction rates, but each type of data may still provide an incomplete picture of diversification dynamics. Here, we combine species-level palaeontological (fossil occurrences) and neontological (molecular phylogenies) data to estimate deep-time diversity dynamics through process-based birth–death models for Carcharhiniformes, the most speciose shark order today. Despite their abundant fossil record dating back to the Middle Jurassic, only a small fraction of extant carcharhiniform species is recorded as fossils, which impedes relying only on the fossil record to study their recent diversification. Combining fossil and phylogenetic data, we recover a complex evolutionary history for carcharhiniforms, exemplified by several variations in diversification rates with an early low diversity period followed by a Cenozoic radiation. We further reveal a burst of diversification in the last 30 million years, which is partially recorded with fossil data only. We also find that reef expansion and temperature change can explain variations in speciation and extinction through time. These results pinpoint the primordial importance of these environmental variables in the evolution of marine clades. Our study also highlights the benefit of combining the fossil record with phylogenetic data to address macroevolutionary questions.

Molecular clocks: Closing the gap between rocks and clocks

Evolution’s past and future: an introduction and partial précis to Stephen Jay Gould’s The Structure of Evolutionary Theory

Carbon isotopes support the presence of extensive land floras pre-dating the origin of vascular plants


 The explore-exploit dilemma is a pervasive problem within the context of social information gathering faced by all individuals. The decision to exploit an old source of information or explore a new source of information involves a trade-off between acquiring new knowledge from the environment to reduce uncertainty (exploration) or immediately receiving rewards (exploitation) (Meder et al., 2020). An important factor influencing information gathering within the context of the explore-exploit dilemma is time. Research has shown that in shorter time horizons, adults are more likely to exploit old sources of information and in longer time horizons, adults are more likely to explore new sources of information. Thus, when given more opportunities to explore, adults perceive the benefits of exploring novel stimuli to outweigh the immediate reward of exploring an old source of information (Wilson et al., 2014). Prior accuracy of the informant has also been shown to influence the decision to explore or exploit sources of information. The current study aims to extend the work of Gutzin (2021) and will consist of two parts; study one will replicate the work of Gutzin (2021) directly, studying adults online. Study two will extend the work of Gutzin (2021) to accommodate an online platform with children. The previous studies examining this effect had small sample sizes and in turn low statistical power. To address this, the current study will be composed of larger sample sizes so that final conclusions regarding this effect can be made. In line with previous literature and studies, it hypothesized that both adults and children will tend to exploit the familiar informant in shorter time horizons and explore the novel informant in longer time horizons and prior accuracy of the familiar informant will affect exploration tendencies.

Recent Fourier analyses of fossil extinction data have indicated that the power spectrum of extinction during the Phanerozoic may take the form of 1/f noise, a result which, it has been suggested, could be indicative of the presence of `critical dynamics' in the processes giving rise to extinction. In this paper we examine extinction power spectra in some detail, using family-level data from two widely available compilations. We find that although the average form of the power spectrum roughly obeys the 1/f law, the spectrum can be represented more accurately by dividing it into two regimes: a low-frequency one which is well fit by an exponential, and a high-frequency one in which it follows a power law with a 1/f2 form. We give explanations for the occurrence of each of these behaviours and for the position of the crossover between them.

On the face of it, deep-time paleoecology—trying to reconstruct species interactions and the flow of matter and energy in a complex ecosystem using nothing more than the remains of long-extinct organisms—seems like folly. Fossil data are biased, time-averaged residues of once-living systems in which it is impossible to directly observe or experimentally manipulate organism interactions. This is simply the nature of historical data; what happened in the past is done and history cannot be rerun. However, just as the study of human history provides examples to understand political, social, and economic dynamics in the present day, the fossil record provides examples that have much to teach us about how modern ecosystems work. In PNAS, Aberhan and Kiessling (1) use the response of benthic marine molluscan assemblages to a severe global perturbation (the end-Cretaceous mass extinction 66 million years ago) to shed light on the complex dynamics of ecological systems.

This chapter is not intended to give a detailed discussion of all we know about eras of stasis and radiation in evolutionary history, but concentrates on a few recent studies that provide evidence for saturation (equilibrium) and nonsaturation (nonequilibrium) in evolutionary history. It also gives a brief account of human impact on diversity. The fossil record and interpretations There have been three marine evolutionary floras and faunas, i.e., the Cambrian, Paleozoic and Modern, each with its own degree of diversity, and each subsequent one with higher diversity than the previous one (Jablonski and Sepkoski 1996). Benton (1995, 1998), re-analysing fossil evidence, has shown that there has been an exponential increase in the number of families of continental and marine organisms in geological time to the Recent. Courtillot and Gaudemer (1996) analysed the same data, and arrived at the somewhat different conclusion that equilibria were reached several times but re-established at higher levels after each mass extinction; but they still found an increase over geological time. Jablonski (1999, see also Jackson and Johnston 2001) has shown that fossil data are solid and that the general trend of increasing diversity has not been changed by more recent data collected between 1982 and 1992 (Figure 6.1): there was a sharp rise in diversity in the Cambrian, a Paleozoic plateau interrupted by several mass extinctions, and a sharp rise since the Triassic, also interrupted by several extinction events.

Summary. The fossil record of the vanation of the solar day and the synodic month with geological time is examined for evidence of the steady contraction of the Earth postulated by Lyttleton to explain a discrepancy between the apparent secular accelerations of the Sun and Moon. Data for the Phanerozoic and the Precambrian agree in showing that a change in the Earth's moment of inertia as large as that suggested by Lyttleton is only consistent with the fossil record if the secular change in the gravitational constant G/C 2 + 4 x 10-/yr. A variation of G of this magnitude appears to be ruled out by a recent analysis of lunar occultation observations utilizing Atomic Time. In a recent analysis of the apparent secular accelerations of the Sun and Moon Lyttleton (1976) has suggested that a discrepancy between observation and the predictions of tidal theory first noted by Jeffreys (1929) may be explained by a steady decrease in the Earth's moment of inertia i/Z = - 8 x lO-/yr. This observation lends support to the phasechange hypothesis (Ramsey 1948; Lyttleton 1965) in which the continued evolution of the Earth's liquid tore leads to a global contraction of order 0.1 mm/yr and a change in the moment of inertia consistent with that required to reconcile the astronomical observations. In this paper I shall discuss whether a contraction of the Earth of this magnitude is consistent with the lengths of the tropical year and the synodic month deduced from the growth patterns found in fossil bivalves, corals and stromatolites. I shall show that the fossil data probably rule out changes in the Earth's moment of inertia as large as those required to resolve the discrepancy between the lunar and solar accelerations.

BackgroundThe fossil record has suggested that clade growth may differ in marine and terrestrial taxa, supporting equilibrial models in the former and expansionist models in the latter. However, incomplete sampling may bias findings based on fossil data alone. To attempt to correct for such bias, we assemble phylogenetic supertrees on one of the oldest clades of insects, the Odonatoidea (dragonflies, damselflies and their extinct relatives), using MRP and MRC. We use the trees to determine when, and in what clades, changes in taxonomic richness have occurred. We then test whether equilibrial or expansionist models are supported by fossil data alone, and whether findings differ when phylogenetic information is used to infer gaps in the fossil record.ResultsThere is broad agreement in family-level relationships between both supertrees, though with some uncertainty along the backbone of the tree regarding dragonflies (Anisoptera). "Anisozygoptera" are shown to be paraphyletic when fossil information is taken into account. In both trees, decreases in net diversification are associated with species-poor extant families (Neopetaliidae, Hemiphlebiidae), and an upshift is associated with Calopterygidae + Polythoridae. When ghost ranges are inferred from the fossil record, many families are shown to have much earlier origination dates. In a phylogenetic context, the number of family-level lineages is shown to be up to twice as high as the fossil record alone suggests through the Cretaceous and Cenozoic, and a logistic increase in richness is detected in contrast to an exponential increase indicated by fossils alone.ConclusionsOur analysis supports the notion that taxa, which appear to have diversified exponentially using fossil data, may in fact have diversified more logistically. This in turn suggests that one of the major apparent differences between the marine and terrestrial fossil record may simply be an artifact of incomplete sampling. Our results also support previous notions that adult colouration plays an important role in odonate radiation, and that Anisozygoptera should be grouped in a single inclusive taxon with Anisoptera, separate from Zygoptera.