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Hall's Cave, Kerr county, Texas. (a) Picture of the site located at 3008N, 9932W at an elevation of 500 m in an area of modest topographical relief. Mean annual temperature is 18C and mean precipitation is 800 mm (Collins 2004); (b, c) hypothesized trophic relationships between extinct and extant mammal fauna in the community are depicted. The ellipse represents the projected isotopic niche space. Values are approximate; they were taken from the literature and may not be representative of Hall's Cave. Note the large number of grazers present in the pre-extinction panel. Grey text in the 'post-extinction' panel represents taxa extirpated by the LP megafauna extinction.
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Recent studies connecting the decline of large predators and consumers with the disintegration of ecosystems often overlook that this natural experiment already occurred. As recently as 14 ka, tens of millions of large-bodied mammals were widespread across the American continents. Within 1000 yr of the arrival of humans, ∼80% were extinct including...
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... we examine the influence of the LP extinction on a mammal community in the southern Great Plains of North America. Our site, Hall's Cave, lies in the center of the Edwards Plateau (Fig. 1), a distinct region of the Texas Hill country dominated by juniper-oak or oak-mesquite savanna with an understory of mid-to short grasslands ). Because of extensive paleontological excavations and comprehensive radiocarbon dating , Cooke et al. 2003, this site has produced an extremely well dated ( 160 AMS radiocar- bon dates) ...
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... the Edward's Plateau supported a diverse mammal assemblage with mammoth, horse, camels and many other megaherbivores, as well as many medium- and small-bodied species that still occur in the region today. The terminal Pleistocene extinction resulted in the loss of 80% of the large-bodied herbivores and 20% of the apex predators in the ecosystem (Fig. 1b). Thus, Hall's Cave pro- vides an unparalleled opportunity to quantitatively examine the influence of the LP megafauna extinction on mammal community structure, and moreover, to potentially disen- tangle the influence of previously recognized fluctuations in late Quaternary climate from biotic interactions such as ...
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... mammal communities are based on Hall's Cave and the 20 nearby fossil sites on the Edward's Plateau of Texas ( Fig. 1; Supplementary material Appendix 1, Table A1). In the Pleistocene, this region supported an open grassland eco- system (Joines 2011). Today, it consists of a juniper-oak/ mesquite-acacia savanna with an understory of short grasses; both rainfall and temperature is intermediate between dry grasslands/savanna eco-regions ( Collins et al. ...
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... camels, etc.), and not through shifts in the minimum size (Fig. 2d). It led to a fundamental restricting of the shape of the BSD from bimodal to flat, and from right, to left skewed (Fig. 2e, Fig. 3). These shifts were correlated with both climate fluctuations and the LP extinction, with an essentially modern BSD established by the Holocene (Fig. 3, Table 1). The shape of the BSD dis- tribution was significantly different at time periods centered on 10.3, 13.8, 15.3-16.5, and 18.8 ka (two-sample K-S tests, p 0.0001; Table 1). This encompassed the terminus of the Younger Dryas cold episode, which was marked by abrupt warming, the onset of the megafauna extinction at 13.8 ka, and the ...
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... anticipated that the loss of apex carnivores would lead to a restructuring of the guild. The modern apex car- nivores in North America (e.g. jaguar, mountain lion, wolf, grizzly bear) were mesocarnivores in the Pleistocene when saber-tooth and scimitar-toothed cats, dire wolves and the short-faced bear dominated the community (Fig. 1). Because apex carnivores are known to be hyper-carnivorous (Van Valkenburg et al. 2004), we expected that they would form (Fig. 2c) coincident with a decrease in the median/mean body mass, neither the minimum nor the maximum body mass changed until 11-12 ka, around the end of the LP extinction event (Fig. 2d). This suggests that ...
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... some changes in the community were clearly the result of the warming climate at the terminal Pleistocene, it is also clear that the loss of 80% of the megaherbivores and 20% of the apex predators (Fig. 1) between 13.8-11.4 ka fundamentally changed the structure of the mammal com- munity at Hall's Cave. In addition to the turnover at 17-18 ka, there is another increase in beta diversity at 12-14 ka coincident with the LP extinction and largely before the YD event (Fig. 2c). This time the increase in beta diversity is accompanied by a ...
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... the community for most of the late Pleistocene record, even during the warming climate associated with the retreat of glaciers in North America (Fig. 4), this abruptly changed with the LP extinction. The proportion of grazers in the system dropped by more than half, with only bison, prong- horn and a few medium-to small-bodied species surviving (Fig. 1). Because large-bodied grazers help maintain grass- lands (Owen-Smith 1987, their absence probably resulted in encroachment of woody vegetation, which may have changed the relative amount of annual C 3 versus C 4 bio- mass production at the site. 14-EV However, we found the opposite: aggregated pairs tended to be more similar in body ...
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... Present-natural ranges for extinct species were generally based on the co-occurrence with multiple surviving species (Faurby et al. 2018). Moreover, many megafauna are known to co-occur and interact, and several lines of evidence suggest that the cooccurrence of mammals was higher during the Late Pleistocene (Smith, Tomé, et al. 2016;Tóth et al. 2019). We also note that the current assemblages are, likewise, based on coarse range maps that may overestimate species co-occurrences and inflate assemblage similarities. ...
Various authors have suggested that extinctions and extirpations of large mammalian herbivores during the last ca. 50,000 years have altered ecological processes. Yet, the degree to which herbivore extinctions have influenced ecosystems has been difficult to assess because past changes in herbivore impact are difficult to measure directly. Here, we indirectly estimated changes in (theorised) herbivore impact by comparing the functional composition of current large (≥ 10 kg) mammalian herbivore assemblages to those of a no‐extinction scenario. As an assemblage's functional composition determines how it interacts with its environment, changes in functional compositions should correspond to changes in ecological impacts. We quantified functional composition using the body mass, diet and life habit of all wild herbivorous mammal species (n = 502) present during the last 130,000 years. Next, we assessed whether these changes in functional composition were large enough that the resulting assemblages could be considered functionally novel. Finally, we assessed where novel herbivore assemblages would most likely lead to changes in biome state. We found that 47% of assemblages are functionally novel, indicating fundamental changes in herbivore impacts occurred across much of the planet. On 20% of land, functionally novel herbivore assemblages have arisen in areas where alternative biome states are possible depending on the disturbance regime. Thus, in many regions, the late‐Quaternary extinctions and extirpations altered herbivore assemblages so profoundly that there were likely major consequences for ecosystem functioning.
... Ecological theory predicts that factors such as invasion and climate change have large effects on community structure (Lomolino 1986;Robinson and Dickerson 1987;Schwindt et al. 2001;Spooner and Vaughn 2008;Smith et al. 2016;Tóth et al. 2019). For example, the composition of Swedish bird communities has changed rapidly in response to varying summer temperatures since the 1960s (Lindström et al. 2013). ...
A central goal in ecology is investigating the impact of major perturbations, such as invasion, on the structure of biological communities. One promising line of inquiry is using co-occurrence analyses to examine how species’ traits mediate coexistence and how major ecological, climatic, and environmental disturbances can affect this relationship and underlying mechanisms. However, present communities are heavily influenced by anthropogenic behaviors and may exhibit greater or lesser resistance to invasion than communities that existed before human arrival. Therefore, to disentangle the impact of individual disturbances on mammalian communities, it is important to examine community dynamics before humans. Here, we use the North American fossil record to evaluate the co-occurrence structure of mammals across the Great American Biotic Interchange. We compiled 126 paleocommunities from the late Pliocene (4–2.5 Ma) and early Pleistocene (2.5–1 Ma). Genus-level co-occurrence was calculated to identify significantly aggregated (co-occur more than expected) and segregated (co-occur less than expected) genus pairs. A functional diversity analysis was used to calculate functional distance between genus pairs to evaluate the relationship between pair association strength and functional role. We found that the strength distribution of aggregating and segregating genus pairs does not significantly change from the late Pliocene to the early Pleistocene, even with different mammals forming the pairs, including immigrant mammals from South America. However, we did find that significant pairs, both aggregations and segregations, became more similar in their functional roles following the Plio-Pleistocene transition. Due to different mammals and ecological roles forming significant associations and the stability of co-occurrence structure across this interval, our study suggests that mammals have fundamental ways of assembling that may have been altered by humans in the present.
... The cave floor consists of over 4 m of stratified cave sediments with a long, well-dated sedimentary, paleoclimate, paleoenvironmental, and paleontological record spanning the entire Holocene and Late Pleistocene , Cooke et al., 2003, Smith et al., 2015, Cordova and Johnson, 2019. The species of bats and mammals reported from the cave vary over this time span resulting in a complex biogeochemical history. ...
This paper presents the results of a study to identify the species and distribution of diatoms growing in various habitats and on different substrates in Hall’s Cave, a limestone cave located on the Edward’s Plateau in western Kerr County, central Texas, USA. A diverse diatom assemblage that includes at least seventeen taxa was found growing in low to very low light conditions in different parts of the cave interior and on the walls of the cave entrance. Many other species were found in low numbers and may have been transported into the cave. One diatom species, Nitzschia palmida Carter is dominant in many samples, and overall, is the most abundant diatom observed in this investigation. This is the f irst published occurrence of N. palmida in the Western Hemisphere. These diatoms, all found typically in wet or damp settings, have adapted to growing in the cave environment. Nine species were common in only one sample, a scraping of wet guano-rich sediment on the floor at the back of the cave. These diatoms either survived passage through the digestive system of bats or were transported to the back of the cave by other means. The abundance and diversity of diatoms in Hall’s Cave suggests that diatoms may have been living in the cave for as long as there has been adequate moisture, nutrients and light, making them potential proxies for paleoenvironmental studies.
... They carry additional information within their structure, in contrast to time series data such as extinction and origination rates, which are ultimately derived from occurrence counts and locality ages. Various methods of fossil co-occurrence analysis have been applied to investigate mammal community responses to Pleistocene climate change (Carotenuto et al. 2016), late-Miocene cooling (Fraser et al. 2015) and Paleocene-Eocene global warming (Fraser and Lyons 2020), characterize communities before and after the end-Pleistocene extinction (Smith et al. 2016), evaluate changes in plant and animal species co-occurrence patterns over the last 300 Ma (Lyons et al. 2016) and quantify ecospace occupation of Mesozoic mammaliaform paleocommunities (Chen et al. 2019). ...
... Bayesian network analysis methods, yielding full distributions of co-occurrence probabilities among different taxa, can be used for closer analysis of paleoecosystems and paleocommunity structure, for instance, species-level interactions between two competing lineages, e.g., Canidae and Felidae (Silvestro et al. 2015), comparison of non-analogous current and Pleistocene communities (Smith et al. 2016), or for investigating the impact of humans during the late Pleistocene and Holocene (Lyons et al. 2016). In addition to this, Bayesian network analysis could be used to infer the probabilities of missing taxa in a locality, thus allowing quantification of taphonomic or collection bias and improving paleontological dataset characterisation. ...
Analysis of fossil assemblage structure can help illuminate the processes shaping the assembly of ecological communities. Using Bayesian network analysis methods, we investigated patterns of association between presences and abundances of 12 large-bodied mammal clades at Pleistocene fossil localities and their dependence on local environment types, global temperature estimates, locality ages and large-scale geographic positions. The dependencies among the clades seem to be structured by the degree of generalism in carnivores and omnivores, inter-specific competition-driven ecological differentiation among the carnivores, and local environmental preferences in herbivores. With the exception of hominids, we do not find significant dependencies among the external variables (gross geographic position, age, mean global temperature) and the clades under investigation. We do not find evidence of exclusion between any two clades, which would indicate predation effects or competition at a family or higher level. The network of dependencies among mammalian clades shows a remarkable lack of change over time, pointing to emergent invariability of taxonomic assemblies at the family or higher level despite significant environmental changes.
... Hall's Cave was first excavated beginning in the late 1960s (then under the name Klein Cave; [12]) and excavations continued in the late 80's-early 90's [10] as well as in recent years [13,14]. Identification of fossil remains from these excavations largely focused on mammalian taxa [10,15,16] and plant microfossils [17], but some herpetofauna were identified, including lizards, snakes, frogs, salamanders, and turtles [10,18]. Previous research on Hall's Cave also included bulk bone ancient DNA metabarcoding analyses, yet lizard ancient DNA was not recovered and amplified [13]. ...
Fossil identification practices have a profound effect on our interpretation of the past because these identifications form the basis for downstream analyses. Therefore, well-supported fossil identifications are necessary for examining the impact of past environmental changes on populations and communities. Here we apply an apomorphic identification framework in a case study identifying fossil lizard remains from Hall’s Cave, a late Quaternary fossil site located in Central Texas, USA. We present images and descriptions of a broad comparative sample of North American lizard cranial elements and compile new and previously reported apomorphic characters for identifying fossil lizards. Our fossil identifications from Hall’s Cave resulted in a minimum of 11 lizard taxa, including five lizard taxa previously unknown from the site. Most of the identified fossil lizard taxa inhabit the area around Hall’s Cave today, but we reinforce the presence of an extirpated species complex of horned lizard. A main goal of this work is to establish a procedure for making well-supported fossil lizard identifications across North America. The data from this study will assist researchers endeavoring to identify fossil lizards, increasing the potential for novel discoveries related to North American lizards and facilitating more holistic views of ancient faunal assemblages.
... A debate exists on the role of climate and humans in the defaunation process. Our hindcasts support previous studies suggesting that climate was the major determinant of species decline in the past 120 000 years (Barnosky et al. 2004, Cooper et al. 2015, Seersholm et al. 2020, as we detected a declining trend in the number of species with sharp transition coinciding with those intervals identified as periods of mammal community reshuffling in Mediterranean regions (~ 20-10 ka BP; VanBuren and Jarzyna 2022), North America (~ 14-11 ka BP; Smith et al. 2016), Holarctic regions (~ 14-11 ka BP; Cooper et al. 2015) and west Eurasia regions (~ 26.5-14 ka BP; Nenzén et al. 2014). Yet our climate-induced hindcasts also depart from trends found in the fossil record since the beginning of the Holocene, particularly when using a baseline that excludes the human effect on mammals' distributional ranges. ...
Studying past community dynamics can provide valuable insights for anticipating future changes in the world's biota. However, the existing fossil record is too sparse to enable continuous temporal reconstructions of wholesale community dynamics. In this study, we utilise machine learning to reconstruct Late Quaternary community structure, leveraging the climate–trophic structure relationship. We followed a four‐stage approach: 1) identify and map trophic structure units (TSUs) at the global scale based on the guild richness and composition of terrestrial mammal species weighing over 3 kg; 2) train a random forest classifier to predict the observed distribution of TSUs based on contemporary climatic conditions; 3) hindcast the global distribution of TSUs using climatic conditions as reconstructed over the past 120 000 years; and 4) compare TSU hindcasts against elements of community structure as estimated with the fossil record. Models project significant shifts in the geographical distribution of community trophic structures, with more pronounced changes occurring during the Pleistocene–Holocene transition. These shifts exhibit regional variations, particularly in Eurasia and North America, where the models project reductions in the distribution of less‐complex trophic structures over the last 24 000 years. Hindcasts partially identified the alterations in community structure seen in the fossil record, demonstrating a match between the observed and predicted times of change in mammal community structure (between 24 and 8 ka BP). However, projections of trophic guilds diverged from fossil records during the Holocene. While the fossil record indicated a decrease in the number of grazers and carnivores, our models projected an increase in these numbers. Characterising community‐wide responses to climatic changes is essential to address key questions about past and future impacts of such changes. Although further research is needed to refine the models, our approach offers a perspective for addressing the complex interactions among climate and trophic structures and model their distributions over time.
... Although it is estimated that more than 500 species of terrestrial vertebrates became extinct during the last century (Ceballos et al., 2020), there are few records of large mammal extinctions globally since the industrial revolution (Ceballos et al., 2020;Pineda-Munoz et al., 2021), and none during the 20th century. By contrast, studies have shown that during the (largely climate dominated) transition at the end of the Pleistocene, many large mammals became extinct while small mammals were more stable (Blois et al., 2010;Smith et al., 2016). The marked difference between extinction patterns at the end of the Pleistocene (loss of large mammal species) and that of the industrial age (their retention) strongly suggests that a human-dominated planet plays by different rules. ...
The Anthropocene's human-dominated habitat expansion endangers global biodiversity. However, large mammalian herbivores experienced few extinctions during the 20th century, hinting at potentially overlooked ecological responses of a group sensitive to global change. Using dental microwear as a proxy, we studied large herbivore dietary niches over a century across mainland China before (1880s–1910s) and after (1970s–1990s) the human population explosion. We uncovered widespread and significant shifts (interspecific microwear differences increased and intraspecific microwear dispersion expanded) within dietary niches linked to geographical areas with rapid industrialization and population growth in eastern China. By contrast, in western China, where human population growth was slower, we found no indications of shifts in herbivore dietary niches. Further regression analysis links the intensity of microwear changes to human land-use expansion. These analyses highlight dietary adjustments of large herbivores as a likely key factor in their adaptation across a century of large-scale human-driven changes.
... Widespread biodiversity loss is more than species extinction; it also leads to the loss of ecological function, which may be realized at local, regional, or even global scales. Large-bodied wild mammals, in particular, play an important role within ecosystems through the transport of nutrients and biogeochemical cycling, modification of vegetation composition and structure, ecological interactions with other animals, and even feedbacks with climate (3,(17)(18)(19)(20)(21)(22)(23). Hence, there is growing concern that the ongoing loss of large-bodied wild mammals may lead to the unraveling of ecosystems because these complex ecological roles are not generally replicated by domesticated or smaller-bodied animals (1)(2)(3)(4)11). ...
... These materials are all housed at the Texas Memorial Museum (TMM) in Austin, TX. The initial faunal list for Hall's Cave was compiled by Toomey (55); our ongoing efforts over the past 4 y with the unidentified fossil materials and recent ancient DNA analysis of sediment (98) from this site have resulted in additional species being recovered (SI Appendix, Table S1) (20). ...
The conservation status of large-bodied mammals is dire. Their decline has serious consequences because they have unique ecological roles not replicated by smaller-bodied animals. Here, we use the fossil record of the megafauna extinction at the terminal Pleistocene to explore the consequences of past biodiversity loss. We characterize the isotopic and body-size niche of a mammal community in Texas before and after the event to assess the influence on the ecology and ecological interactions of surviving species (>1 kg). Preextinction, a variety of C4 grazers, C3 browsers, and mixed feeders existed, similar to modern African savannas, with likely specialization among the two sabertooth species for juvenile grazers. Postextinction, body size and isotopic niche space were lost, and the δ13C and δ15N values of some survivors shifted. We see mesocarnivore release within the Felidae: the jaguar, now an apex carnivore, moved into the specialized isotopic niche previously occupied by extinct cats. Puma, previously absent, became common and lynx shifted toward consuming more C4-based resources. Lagomorphs were the only herbivores to shift toward C4 resources. Body size changes from the Pleistocene to Holocene were species-specific, with some animals (deer, hare) becoming significantly larger and others smaller (bison, rabbits) or exhibiting no change to climate shifts or biodiversity loss. Overall, the Holocene body-size-isotopic niche was drastically reduced and considerable ecological complexity lost. We conclude biodiversity loss led to reorganization of survivors and many "missing pieces" within our community; without intervention, the loss of Earth's remaining ecosystems that support megafauna will likely suffer the same fate.
... The Pliocene and Pleistocene evolution of large herbivores megafauna, such as proboscideans, edentates, camelids, and horses, sparked the co-evolution of various specialized predators, scavengers, parasites, etc. 10,11 , many of which went extinct along with the megaherbivores at the end of the Pleistocene. In the Americas alone, this was the fate of more than thirty species of mammalian and avian predators and scavengers 12,13 . ...
The New World Vulture [Coragyps] occidentalis (L. Miller, 1909) is one of many species that were extinct by the end of the Pleistocene. To understand its evolutionary history we sequenced the genome of a 14,000 year old [Coragyps] occidentalis found associated with megaherbivores in the Peruvian Andes. occidentalis has been viewed as the ancestor, or possibly sister, to the extant Black Vulture Coragyps atratus, but genomic data shows occidentalis to be deeply nested within the South American clade of atratus. Coragyps atratus inhabits lowlands, but the fossil record indicates that occidentalis mostly occupied high elevations. Our results suggest that occidentalis evolved from a population of atratus in southwestern South America that colonized the High Andes 300 to 400 kya. The morphological and morphometric differences between occidentalis and atratus may thus be explained by ecological diversification following from the natural selection imposed by this new and extreme, high elevation environment. The sudden evolution of a population with significantly larger body size and different anatomical proportions than atratus thus constitutes an example of punctuated evolution. 14,000 year old DNA reveals the evolutionary dynamics and adaptations of South American vultures.
... Furthermore, the effects of downsizing and coextinctions could be amplified by possible impacts of future climate change on body size that have also been hypothesized to lead to smaller body mass in mammals (for example, Hoy et al. 44 ) and ectotherms 45 . The predicted future decline and extinction of wild mammals described in this study, which is likely underestimated by not including coextinctions, could generate strong ecological and trophic consequences for wilderness areas, comparable to those triggered by past megafaunal extinctions 18,[46][47][48][49] . Moreover, these changes are currently being seen in marine environments, such as the loss of otters in Pacific kelp ecosystems 37,50 . ...
Diet and body mass are inextricably linked in vertebrates: while herbivores and carnivores have converged on much larger sizes, invertivores and omnivores are, on average, much smaller, leading to a roughly U-shaped relationship between body size and trophic guild. Although this U-shaped trophic-size structure is well documented in extant terrestrial mammals, whether this pattern manifests across diverse vertebrate clades and biomes is unknown. Moreover, emergence of the U-shape over geological time and future persistence are unknown. Here we compiled a comprehensive dataset of diet and body size spanning several vertebrate classes and show that the U-shaped pattern is taxonomically and biogeographically universal in modern vertebrate groups, except for marine mammals and seabirds. We further found that, for terrestrial mammals, this U-shape emerged by the Palaeocene and has thus persisted for at least 66 million years. Yet disruption of this fundamental trophic-size structure in mammals appears likely in the next century, based on projected extinctions. Actions to prevent declines in the largest animals will sustain the functioning of Earth’s wild ecosystems and biomass energy distributions that have persisted through deep time.
