Publications by authors named "Cindy V Looy"

11 Publications

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

Syst Biol 2021 Mar 24. Epub 2021 Mar 24.

University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA 94709, USA.

Phylogenetic 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 mid-Devonian and Late 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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http://dx.doi.org/10.1093/sysbio/syab020DOI Listing
March 2021

Investigating Biotic Interactions in Deep Time.

Trends Ecol Evol 2021 01 13;36(1):61-75. Epub 2020 Oct 13.

School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.

Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.
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http://dx.doi.org/10.1016/j.tree.2020.09.001DOI Listing
January 2021

The base of the Lystrosaurus Assemblage Zone, Karoo Basin, predates the end-Permian marine extinction.

Nat Commun 2020 03 18;11(1):1428. Epub 2020 Mar 18.

Department of Geology, Amherst College, Amherst, MA, 01002, USA.

The current model for the end-Permian terrestrial ecosystem crisis holds that systematic loss exhibited by an abrupt turnover from the Daptocephalus to the Lystrosaurus Assemblage Zone (AZ; Karoo Basin, South Africa) is time equivalent with the marine Permian-Triassic boundary (PTB). The marine event began at 251.941 ± 0.037 Ma, with the PTB placed at 251.902 ± 0.024 Ma (2σ). Radio-isotopic dates over this interval in the Karoo Basin were limited to one high resolution ash-fall deposit in the upper Daptocephalus AZ (253.48 ± 0.15 (2σ) Ma) with no similar age constraints for the overlying biozone. Here, we present the first U-Pb CA-ID-TIMS zircon age (252.24 ± 0.11 (2σ) Ma) from a pristine ash-fall deposit in the Karoo Lystrosaurus AZ. This date confirms that the lower exposures of the Lystrosaurus AZ are of latest Permian age and that the purported turnover in the basin preceded the end-Permian marine event by over 300 ka, thus refuting the previously used stratigraphic marker for terrestrial end-Permian extinction.
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http://dx.doi.org/10.1038/s41467-020-15243-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080820PMC
March 2020

UV-B-induced forest sterility: Implications of ozone shield failure in Earth's largest extinction.

Sci Adv 2018 02 7;4(2):e1700618. Epub 2018 Feb 7.

Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, 3060 Valley Life Sciences Building, Berkeley, CA 94720-3140, USA.

Although Siberian Trap volcanism is considered a primary driver of the largest extinction in Earth history, the end-Permian crisis, the relationship between these events remains unclear. However, malformations in fossilized gymnosperm pollen from the extinction interval suggest biological stress coinciding with pulsed forest decline. These grains are hypothesized to have been caused by enhanced ultraviolet-B (UV-B) irradiation from volcanism-induced ozone shield deterioration. We tested this proposed mechanism by observing the effects of inferred end-Permian UV-B regimes on pollen development and reproductive success in living conifers. We find that pollen malformation frequencies increase fivefold under high UV-B intensities. Surprisingly, all trees survived but were sterilized under enhanced UV-B. These results support the hypothesis that heightened UV-B stress could have contributed not only to pollen malformation production but also to deforestation during Permian-Triassic crisis intervals. By reducing the fertility of several widespread gymnosperm lineages, pulsed ozone shield weakening could have induced repeated terrestrial biosphere destabilization and food web collapse without exerting a direct "kill" mechanism on land plants or animals. These findings challenge the paradigm that mass extinctions require kill mechanisms and suggest that modern conifer forests may be considerably more vulnerable to anthropogenic ozone layer depletion than expected.
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http://dx.doi.org/10.1126/sciadv.1700618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5810612PMC
February 2018

Holocene shifts in the assembly of plant and animal communities implicate human impacts.

Nature 2016 Jan 16;529(7584):80-3. Epub 2015 Dec 16.

Department of Biology, University of Vermont, Burlington, Vermont 05405, USA.

Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size and the spread of agriculture in North America. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity.
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http://dx.doi.org/10.1038/nature16447DOI Listing
January 2016

Spatiotemporal relationships among Late Pennsylvanian plant assemblages: Palynological evidence from the Markley Formation, West Texas, U.S.A.

Rev Palaeobot Palynol 2014 Dec;211:10-27

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, United States ; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, United States.

The Pennsylvanian lowlands of western Pangea are best known for their diverse wetland floras of arborescent and herbaceous ferns, and arborescent horsetails and clubmosses. In apparent juxtaposition, a very different kind of flora, dominated by a xerophilous assemblage of conifers, taeniopterids and peltasperms, is occasionally glimpsed. Once believed to represent upland or extrabasinal floras from well-drained portions of the landscape, these dryland floras more recently have been interpreted as lowland assemblages growing during drier phases of glacial/interglacial cycles. Whether Pennsylvanian dryland and wetland floras were separated spatially or temporally remains an unsettled question, due in large part to taphonomic bias toward preservation of wetland plants. Previous paleobotanical and sedimentological analysis of the Markley Formation of latest Pennsylvanian (Gzhelian) age, from north central Texas, U.S.A, indicates close correlation between lithofacies and distinct dryland and wetland megaflora assemblages. Here we present a detailed analysis one of those localities, a section unusual in containing abundant palynomorphs, from the lower Markley Formation. Paleobotanical, palynological and lithological data from a section thought to represent a single interglacial/glacial phase are integrated and analyzed to create a complex picture of an evolving landscape. Megafloral data from throughout the Markley Formation show that conifer-dominated dryland floras occur exclusively in highly leached kaolinite beds, likely eroded from underlying soils, whereas a mosaic of wetland floras occupy histosols, ultisols, and fluvial overbank deposits. Palynological data largely conform to this pattern but reveal a more complex picture. An assemblage of mixed wetland and dryland palynofloral taxa is interpolated between a dryland assemblage and an overlying histosol containing wetland taxa. In this section, as well as elsewhere in the Markley Formation, kaolinite and overlying organic beds appear to have formed as a single genetic unit, with the kaolinite forming an impermeable aquiclude upon which a poorly drained wetland subsequently formed. Within a single inferred glacial/interglacial cycle, lithological data indicate significant fluctuations in water availability tracked by changes in palynofloral and megafloral taxa. Palynology reveals that elements of the dryland floras appear at low abundance even within wetland deposits. The combined data indicate a complex pattern of succession and suggest a mosaic of dryland and wetland plant communities in the Late Pennsylvanian. Our data alone cannot show whether dryland and wetland assemblages succeed one another temporally, or coexisted on the landscape. However, the combined evidence suggests relatively close spatial proximity within a fragmenting and increasingly arid environment.
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http://dx.doi.org/10.1016/j.revpalbo.2014.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443493PMC
December 2014

Evidence for coal forest refugia in the seasonally dry Pennsylvanian tropical lowlands of the Illinois Basin, USA.

PeerJ 2014 4;2:e630. Epub 2014 Nov 4.

College of Life and Environmental Sciences, University of Exeter , Exeter, Devon , UK.

The Moscovian plant macroflora at Cottage Grove southeastern Illinois, USA, is a key example of Pennsylvanian (323-299 Million years ago) dryland vegetation. There is currently no palynological data from the same stratigraphic horizons as the plant macrofossils, leaves and other vegetative and reproductive structures, at this locality. Consequently, reconstructions of the standing vegetation at Cottage Grove from these sediments lack the complementary information and a more regional perspective that can be provided by sporomorphs (prepollen, pollen, megaspores and spores). In order to provide this, we have analysed the composition of fossil sporomorph assemblages in two rock samples taken from macrofossil-bearing inter-coal shale at Cottage Grove. Our palynological data differ considerably in composition and in the dominance-diversity profile from the macrofossil vegetation at this locality. Walchian conifers and pteridosperms are common elements in the macroflora, but are absent in the sporomorph assemblages. Reversely, the sporomorph assemblages at Cottage Grove comprise 17 spore taxa (∼16% and ∼63% of the total assemblages) that are known from the lycopsid orders Isoetales, Lepidodendrales and Selaginallales, while Cottage Grove's macrofloral record fails to capture evidence of a considerable population of coal forest lycopsids. We interpret our results as evidence that the Pennsylvanian dryland glacial landscape at Cottage Grove included fragmented populations of wetland plants living in refugia.
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http://dx.doi.org/10.7717/peerj.630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226648PMC
November 2014

Environmental mutagenesis during the end-Permian ecological crisis.

Proc Natl Acad Sci U S A 2004 Aug 28;101(35):12952-6. Epub 2004 Jul 28.

Laboratory of Palaeobotany and Palynology, Utrecht University, Budapestlaan 4, 3584 CD Utrecht, The Netherlands.

During the end-Permian ecological crisis, terrestrial ecosystems experienced preferential dieback of woody vegetation. Across the world, surviving herbaceous lycopsids played a pioneering role in repopulating deforested terrain. We document that the microspores of these lycopsids were regularly released in unseparated tetrads indicative of failure to complete the normal process of spore development. Although involvement of mutation has long been hinted at or proposed in theory, this finding provides concrete evidence for chronic environmental mutagenesis at the time of global ecological crisis. Prolonged exposure to enhanced UV radiation could account satisfactorily for a worldwide increase in land plant mutation. At the end of the Permian, a period of raised UV stress may have been the consequence of severe disruption of the stratospheric ozone balance by excessive emission of hydrothermal organohalogens in the vast area of Siberian Traps volcanism.
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http://dx.doi.org/10.1073/pnas.0404472101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC516500PMC
August 2004