Charles R. Marshall’s research while affiliated with University of California, Berkeley and other places

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Publications (94)


All unfiltered (i.e. not spatially unique) Glyptotherium fossil localities used in this analysis, with their approximate ages indicated by the colors: Rancholabrean (0.014–0.240 Ma; green points), n = 85; Irvingtonian (0.240–1.806 Ma; blue points), n = 14; Blancan (1.806–4.75 Ma; purple points), n = 25. Possible migration routes from South America to North America for Glyptotherium: the ‘high road' through the Andes (1), the ‘low road' around the Amazon rainforest (2), or rafting through the Antilles (3). Once through Central America and Mexico (4), Glyptotherium could have expanded to the north (5), or stayed in the ‘Gulf Coast Savanna Corridor' (6). Figure made in collaboration with Miranta Kouvari (Science Graphic Design). See the Material and methods section for details of the data compilation, and the Supporting information for details on localities.
Median suitable conditions for Glyptotherium calibrated in the Rancholabrean using 24 spatially unique occurrences, projected to the Late and Middle Blancan and Blancan‐Hemphillian. The LTP and maxSSS maps are examples of more and less conservative threshold estimates for suitable conditions, respectively. The orange points represent spatially filtered Glyptotherium localities for the Rancholabrean and the red and blue points are the independent testing localities for the projections. Consensus models for the Rancholabrean: 0.112 Ma, Late Blancan: ~2.19 Ma, Middle Blancan: ~3.09 Ma, and Blancan‐Hemphillian: ~4.47 Ma. Light purple indicates suitable conditions and gray indicates non‐suitable conditions for Glyptotherium. LTP and MaxSSS points in blue lie in places predicted to have suitable environmental conditions, whereas points in red are not (note that many of the occurrences overlap spatially at this scale for the Late and Middle Blancan intervals).
Results of the movement corridor analysis for South America during the Blancan‐Hemphillian (~4.47 Ma). From left to right: raster map of ENM results for suitable conditions; red line showing least‐cost path model; raster map of connectivity values from the circuit theory model (the color scale is histogram‐equalized). Black triangles represent the start and end points for the models.
Evaluating migration hypotheses for the extinct Glyptotherium using ecological niche modeling
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January 2025

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Charles R. Marshall

The formation of the Isthmus of Panama allowed for migrations between the once separated continents of North and South America. This led to one of the greatest documented interchanges of biota in Earth history, wherein an array of species across many groups migrated between the continents. Glyptotherium, a giant extinct armadillo‐like grazer, is an example of a taxon that likely originated in South America and migrated to North America. Here we use Ecological niche modeling to test the extent of suitable conditions for Glyptotherium in Central America and surrounding regions during the intervals when the taxon is thought to have dispersed, allowing for assessment of plausible migration routes and the hypothesis that the genus migrated from North America back to South America during the Rancholabrean (14 000–240 000 years ago). Our niche modeling results show suitable abiotic conditions for Glyptotherium in Central America and the surrounding area throughout the Plio‐Pleistocene, with western South America (the ‘high road') suggested as their ancestors' route northwards. Depending on the extent of suitable conditions, it may have been possible for Glyptotherium to return to South America during the Rancholabrean. The results support previous hypotheses that the range of Glyptotherium was constrained by the need for warm, wet environments.

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Evolutionary allometry of the canid baculum (Carnivora: Mammalia)

June 2024

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28 Reads

Biological Journal of the Linnean Society

While the mammalian baculum shows enormous morphological variability, the baculum of canids is highly conserved, with most variation restricted to size. Here, we explore the allometric relationship between baculum length and body size in extant and extinct canids. Examination of 26 species in the extant subfamily Caninae using standard linear regression revealed isometry. Phylogenetic regression also revealed an allometric slope indistinguishable from isometry. This pattern differs from the substantially negative slopes seen in other mammalian clades. The strength of the canid allometric relationship (r2) is also greater than in other clades, suggesting functional constraints on their baculum size. The constraints may be related to the copulatory tie that is characteristic of canids, and/or their monogamous mating system. Complete bacula are known from just four extinct species. The two complete bacula from the extinct subfamily Borophaginae (Aelurodon ferox and Aelurodon stirtoni) fall on the same allometric relationship as the living canids. However, the baculum of the extinct dire wolf (Aenocyon dirus, from the extant subfamily Caninae) and from the extinct subfamily Herperocyoninae, Hesperocyon gregarius, are significantly longer than expected based on their body sizes, suggesting that they may have had a different reproductive biology from that of extant canines.


Quantitative evidence for dimorphism suggests sexual selection in the maxillary caniniform process of Placerias hesternus

May 2024

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122 Reads

Placerias hesternus, a Late Triassic dicynodont, is one of the last megafaunal synapsids of the Mesozoic. The species has a tusk-like projection on its maxillary bone, known as the caniniform process. This process has been hypothesized to be sexually dimorphic since the 1950s, however this claim has not been thoroughly investigated quantitatively. Here, we examined maxillae, premaxillae, quadrates, and fibulae from a single population from the Placerias Quarry in the Blue Mesa Member of the Chinle Formation, near St. Johns, Arizona, USA to determine if the caniniform process is dimorphic. We made a total of 25 measurements from the four bones and used a maximum likelihood framework to compare the fit of unimodal versus bimodal distributions for each set of measurements. Our results from complete maxillae reveal that the caniniform process has two distinct morphs, with a shorter and longer form. This interpretation is substantiated both by strong statistical support for bimodal distribution of caniniform lengths, and by clustering analysis that clearly distinguishes two morphs for the maxillae. Clustering analysis also shows support for potential dimorphism in the shape of the quadrate. However, no measurements from elements other than the maxilla have a strong likelihood of bimodal distribution. These results support the long-standing hypothesis that the caniniform in Placerias was dimorphic. Alternative explanations to sexual dimorphism that could account for the dimorphism among these fossils include the presence of juveniles in the sample or time-averaged sampling of a chronospecies, but both have been previously rejected for the Placerias Quarry population. The lack of strong dimorphism in non-maxilla elements and increased variation in caniniform length of the large-caniniform morph suggest that the caniniform is a secondary sexual trait, possibly used in intraspecific competition.


Figure 2. (A) It seems likely that the first ribozymes were generated by chance through the hybridization and spontaneous ligation of RNA oligonucleotides (blue and red strands) which produced an RNA ligase (blue strand). (B) With the evolution of a ribozyme capable of ligating RNA oligonucleotides (folded blue strand), production of ribozymes would have been greatly accelerated.
Figure 6. Living linages of bacteria, archaea, and eukaryotes are depicted over time (toward the outer portion of the diagram). LUCA, the Last Universal Common Ancestor of these living species, is depicted as existing in a vent system prior to the emergence of bacteria and archaea. There was an extensive lateral gene transfer between lineages, particularly those bacterial and archaeal (insert). Eukaryotes resulted from the merger of a bacterium and an archaeon [161]. After the development of eukaryotes, secondary symbioses led to photosynthetic eukaryotes. Many lineages likely became extinct over time, but are not depicted. Figure reproduced from [21] with permission from the author.
Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell

February 2024

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307 Reads

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2 Citations

Life

The path from life’s origin to the emergence of the eukaryotic cell was long and complex, and as such it is rarely treated in one publication. Here, we offer a sketch of this path, recognizing that there are points of disagreement and that many transitions are still shrouded in mystery. We assume life developed within microchambers of an alkaline hydrothermal vent system. Initial simple reactions were built into more sophisticated reflexively autocatalytic food-generated networks (RAFs), laying the foundation for life’s anastomosing metabolism, and eventually for the origin of RNA, which functioned as a genetic repository and as a catalyst (ribozymes). Eventually, protein synthesis developed, leading to life’s biology becoming dominated by enzymes and not ribozymes. Subsequent enzymatic innovation included ATP synthase, which generates ATP, fueled by the proton gradient between the alkaline vent flux and the acidic sea. This gradient was later internalized via the evolution of the electron transport chain, a preadaptation for the subsequent emergence of the vent creatures from their microchamber cradles. Differences between bacteria and archaea suggests cellularization evolved at least twice. Later, the bacterial development of oxidative phosphorylation and the archaeal development of proteins to stabilize its DNA laid the foundation for the merger that led to the formation of eukaryotic cells.



James Valentine (20 November 1926–7 April 2023), co-founder of Paleobiology and master of idiographically informed nomothetism

August 2023

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114 Reads

Paleobiology

In 1980, Steven J. Gould published an essay on the emergence of paleobiology as a nomothetic discipline (Gould 1980), nomothetism referring to the search for general laws or principles. Gould contrasted this with the foundation of paleontology, the idiographic tradition of detailing the history of life from the description of new fossil taxa to the elucidation of the long-term patterns of change through time. Among the pioneers of this nomothetic expansion was Jim Valentine. Here I pay tribute to Jim as one of the first paleobiologists, a colleague, coauthor, and friend, emphasizing his intellectual style and insights as much as his lasting contributions. I have written this in part as a eulogy, a remembrance for those who knew him, but also as an introduction to the continuing relevance of his work for those who may be unfamiliar with it.


Stage-by-stage diversity trajectories of marine genera (top panel) and families (bottom panel) derived from Sepkoski’s compendia. The Big Five Mass Extinctions, inferred from an analysis of the extinction rates (data not shown, but see Figures 2 and 3), are indicated by the arrows. They correspond to the times of largest diversity loss. Note that in the genus-level data the Devonian consists of two peaks, indicating that the Late Devonian is more complex than the other big extinctions. Figure modified from Sepkoski (1997).
Substage-by-substage pattern of extinction intensities of marine genera from Bambach’s (2006) analysis of Sepkoski’s compendium, showing the 18 local peaks Bambach defined as mass extinctions. The trajectory shows the pervasiveness of extinction inferred from Sepkoski’s data prior to attempts to compensate for the incompleteness of the fossil record (Figure 3). The higher temporal resolution used compared with Sepkoski’s analyses (Figure 1) suggests that the Capitanian extinction (peak 10) is distinct from the end-Permian extinction (peak 11, the Changhsingian), rather than just being the smearing back of the end-Permian extinction due to the Signor-Lipps effect as was initially thought. Figure reproduced with permission from Bambach (2006) from Annual Reviews.
Two different methods for compensating for the incompleteness of the marine genus fossil record, each applied to different data sets, yield strikingly similar patterns of stage-bystage marine Phanerozoic per genus extinction rates (genus extinctions/genus/million years). The similarities include the timing and relative magnitudes of the peaks, and the timing of (some of) the stages with zero or close to zero extinction rates. Top Panel: From Foote (2007), based on his analysis of Sepkoski’s compendium (Foote, 2003). Bottom Panel: From Kocsis et al. (2019) using the Paleobiology Database. The shading guides the eye to the period boundaries. Ma = millions of years ago.
Classification of mass extinction types
Forty Years Later – The Status of the ‘Big Five’ Mass Extinctions

January 2023

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817 Reads

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21 Citations

Over 40 years ago, Raup and Sepkoski identified five episodes of elevated extinction in the marine fossil record that were thought to be statistically distinct, thus warranting the term the “Big Five” mass extinctions. Since then, the term has become part of standard vocabulary, especially with the naming of the current biodiversity crisis as the “sixth mass extinction.” However, there is no general agreement on which time intervals should be viewed as mass extinctions, in part because the Big Five turn out not to be statistically distinct from background rates of extinction, and in part, because other intervals of time have even higher extinction rates, in the Cambrian and early Ordovician. Nonetheless, the Big Five represent the five largest events since the early Ordovician, including in analyses that attempt to compensate for the incompleteness of the fossil and rock records. In the last 40 years, we have learned a great deal about the causes of many of the major and minor extinction events and are beginning to unravel the mechanisms that translated the initial environmental disturbances into extinction. However, for many of the events, further understanding will require going back to the outcrop, where the patchy distribution of environments and pervasive temporal gaps in the rock record challenge our ability to establish true extinction patterns. As for the current biodiversity crisis, there is no doubt that the rate of extinction is among the highest ever experienced by the biosphere, perhaps the second highest after the end-Cretaceous bolide impact. However (and fortunately), the absolute number of extinctions is still relatively small – there is still time to prevent this becoming a genuine mass extinction. Given the arbitrariness of calling out the Big Five, perhaps the current crisis should be called the “incipient Anthropocene mass extinction” rather than the “sixth mass extinction.”





Citations (69)


... Brunk and Marshall review how reflexively autocatalytic food-generated networks led to the origin of eukaryotic cells. In particular, they suggest that because bacteria and archaea are so different, cellularization likely evolved twice, eventually leading to the emergence of eukaryotes via the fusion of bacteria and archaea [5]. Yarus presents a computational study which investigates the origin of the standard genetic code. ...

Reference:

Various Viewpoints to Investigate the Origins of Life Are Needed
Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell

Life

... It is possible, however, to estimate both the origination and extinction times for a given lineage using stratigraphic intervals, which are models that describe these times as parameters that are a function of the pattern of fossil occurrences in time (Strauss and Sadler 1989). Multiple methods exist and are based on different assumptions about the pattern or process that generates the fossil occurrences (Marshall 2010). One of these methods is the Beta-adaptive model (Wang et al. 2016) which can be used when the preservation potential is unknown given a sample of occurrences in time for a given lineage. ...

Using Confidence Intervals to Quantify the Uncertainty in the End-Points of Stratigraphic Ranges
  • Citing Article
  • July 2017

The Paleontological Society Papers

... Elder (1989) has documented a step-wise pattern to the C-T extinction, and the eTo appears somewhat similar from the available data. Although it has been argued from statistical perspectives that gradual or step-wise data may be solely a stratigraphic artifact (Koch, 1991;Marshall, 1995), the analysis by Marshall et al. (1996) of the C-T data suggests that the stratigraphic pattern seen from the collected data is real. This may not be the case for the eTo; some geochemical evidence (see below) suggests that the eTo repopulation may have been somewhat more rapid than the stratigraphic data portray. ...

Confidence Intervals On Stratigraphic Ranges Based On Discrete Sampling, and the Cenomanian/Turonian Boundary Extinctions in the Western Interior Seaway, U.S.A.
  • Citing Article
  • July 2017

The Paleontological Society Special Publications

... Whether the extinction involved two distinct pulses or a protracted interval packaged into pulses by sedimentary hiatuses, this unexpected separation in time and taxonomy should inform models for the extinction and its consequences (Holland and Patzkowsky 2015). At larger scales, a model optimizing origination, extinction, and sampling sharpens extinction events to the point that the end-Guadalupian and mid-Miocene extinction pulses fade to statistical insignificance as backward-smearing of larger events or perhaps regional episodes (Foote 2007;Wang et al. 2014;Fan et al. 2020;Marshall 2023). Sharpening of taxon stratigraphic ranges necessarily feeds back on the interpretation of extinction drivers and their selectivity, which can in turn prompt further examination of stratigraphic ranges (see Holland [2020] for an overview of new approaches to the stratigraphy of mass extinctions). ...

Forty Years Later – The Status of the ‘Big Five’ Mass Extinctions

... In other words, we do not know how to ask good questions, or how to recognize good answers [2]. Here, we propose a set of guidelines (see also [3,4]), and use these to outline a plausible scenario, relying heavily on the novel mechanism of autocatalytic selection. We use these guidelines to propose routes leading from simple starting materials to sugar phosphates, lipids, amino acids, nucleotides, and their polymers (in particular, proteins). ...

‘Whole Organism’, Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life

Life

... Current network models of cascading secondary extinctions chronically underestimate dynamic impacts because they lack feedback processes Williams, 2009, Bodini et al., 2009], whereas available feedback models can be improved with incorporation of expanded species functional traits [Roopnarine et al., 2017, Huang et al., 2023. Suitable models that simulate community dynamics require parameters that are difficult to gather or infer for fossil taxa, such as population sizes [but see Marshall et al., 2021], intrinsic rates of population increase, mortality rates, and interaction strengths, but recent advances that rely largely on scaling relationships of modern taxa and uniformitarian assumptions, plus increasingly sophisticated inferences from fossils themselves, place enhanced models well within reach. ...

Absolute abundance and preservation rate of Tyrannosaurus rex
  • Citing Article
  • April 2021

Science

... Overall, the great bulk of the mass extinction literature research has been on potential drivers, particularly the marshaling of physical and chemical evidence around the major events. In Paleobiology, papers have mainly addressed analytical approaches to the imperfections of the paleobiological record, such as confidence limits on stratigraphic ranges (e.g., Marshall 1997;Wang et al. 2016;Zimmt et al. 2021), and the perpetual issue of extinction selectivity. ...

Recognizing pulses of extinction from clusters of last occurrences
  • Citing Article
  • September 2020

Palaeontology

... Ma) based on previous age estimates (Jażdżewski and Kupryjanowicz 2010); (ii) the root of the family Gammaridae was set to a uniform distribution (110-40 Ma), based on maximum (Hou, Sket, and Li 2014) and minimum (Copilaş-Ciocianu, Borko, and Fišer 2020) dates determined for the family; (iii) the common ancestor of Sarthrogammarus, Comatogammarus, Barnardorium, Relictogammarus, and Rhipidogammarus was set to a normal distribution (mean 38, sigma 2.0, 41.9-34.1 Ma), based on the timing of the retreat of the Tethys Sea (Popov et al. 2004); (iv) the common ancestors of the members of the Lake Ohrid Gammarus clade were set to a normal distribution (mean 1.36, sigma 0.5, 2.34-0.38 Ma) based on the timing of the lake's formation (Wilke et al. 2020) and estimations by Wysocka et al. (2013). MCMC simulations were run for 50 million generations and sampled every 1000 generations. ...

Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem

Science Advances

... This is due to both temporal and spatial bias in the fossil record, which implies that the earliest known fossils are almost certainly younger than the first living members of the families. Meanwhile, some of the methods for establishing maximum ages based on the fossil record have been proposed, which take into account fossil richness, average paleontological species duration and preservation potential (Marshall, 2019), but none of which has to our knowledge been applied to Hymenoptera yet. ...

Using the Fossil Record to Evaluate Timetree Timescales

... The Hawaiian archipelago is home to the largest concentration of Peperomia species in the Pacific (Lim et al. 2019). There are 23 endemic and two indigenous species found in Hawai'i most growing as epiphytes or terrestrials in mesic valleys to wet forests (Wagner et al. 1999). ...

Multiple colonizations of the Pacific by Peperomia (Piperaceae): Complex patterns of long‐distance dispersal and parallel radiations on the Hawaiian Islands
  • Citing Article
  • September 2019

Journal of Biogeography