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The hidden legacy of megafaunal extinction: loss of functional diversity and resilience over the late Quaternary at Hall’s Cave


Hedberg, Carson P. (2022), The hidden legacy of megafaunal extinction: loss of functional diversity and resilience over the late Quaternary at Hall’s Cave, Dryad, Dataset,


This dataset contains trait data and R code used in the analysis for the paper “Hedberg, C.P., Lyons S.K., & Smith F.A. (2021). THe Hidden Legacy of megafaunal extinction: loss of functional diversity and resilience over the Late Quaternary at Hall's Cave. Global Ecology and Biogeography.”

We collected data for eight functional traits (mass, diet, arboreality, cursoriality, soil disturbance, group size, activity period, migration habit) that collectively describe a species’ ecological role and influence on ecosystem processes. With these data, we investigated changes in functional diversity and redundancy of a local mammal community over time at Hall’s Cave, a site in Central Texas with a continuous record from 21,000 years ago to the present. Additionally, we included several common introduced and domestic species to the modern community to test whether they restore some lost ecological function. 

We found that declines in functional diversity were greater than expected given the decrease in species richness, implying lost taxa contributed higher than average distinct ecological function. Functional distances between remaining species increased through time leading to lowered functional redundancy in younger communities. However, recently introduced taxa increased functional diversity to levels similar to the Holocene and partially restored functional space occupied by Late Pleistocene fauna. Our local-scale analysis demonstrates how prolonged biodiversity erosion not only leads to functionally depauperate communities, but critically lowers ecological resilience to future disturbance.


For this analysis, we collected data on the following traits (variable type): Body mass (numeric), Diet (numeric, percent components), level of cursoriality (ordinal), level of arboreality (ordinal), level of soil disturbance (ordinal), social group size (numeric), activity period (categorical), and migration habit (binary).

Diet was split into percentage components of browse, graze, fruit/grain, vertebrates and invertebrates. For modern species, dietary percentages were estimated from published studies using gut contents or similar methods quantifying specific components of the diet. Studies from populations in Texas were preferred, followed by regions with habitat similar to that found on the Edward’s Plateau. If multiple relevant studies were found for a single species, average values of each component were calculated. For extinct species, dietary percentages were estimated primarily based on stable isotope values from Hall’s Cave specimens and augmented with additional published isotope data when necessary. For herbivorous and omnivorous taxa, in particular, we considered additional published sources of evidence when determining dietary components, including dental microwear texture analysis, morphology, and comparison with modern analogues.

Body mass (in grams) was obtained from MOM v.4.1 (Smith, Lyons, et al., 2003), a global database of Late Quaternary mammal body masses, and log10‐transformed because of substantial variation in size among taxa. Arboreality, cursoriality and soil disturbance were treated as ordinal variables ranked from one to four, with four the highest level. Soil disturbance incorporates the level of fossoriality in addition to other behaviours that affect biopedturbation, such as rutting, wallowing, and digging for food. We defined activity period as a categorical variable with four classifications: diurnal, nocturnal, crepuscular and arrhythmic. Social group size refers to the average number of individuals in conspecific groups cooperatively sharing space and/or resources, not including groups of a mother and offspring. We estimated social group size as a continuous variable; this too was log10‐transformed because of high variance among taxa. Finally, migration habit was treated as a binary variable representing migratory (one) and non‐migratory (zero) taxa. For taxa evaluated at the generic level where several potential species were present, we used an average of the trait values for these species. In all cases, individual species within the genus were functionally similar; hence, the average values are characteristic of the functional role of any potential member.

Trait data for all taxa was determined from peer‐reviewed literature sources. A full list of these sources as well as further details of how trait values were determined can be found in the Supporting Information section of this dataset’s associated publication.

The mammalian fauna at Hall’s Cave were split into six distinct temporal communities: the Terminal Pleistocene (TP) from 21,000 to 11,700 BP; the Early Holocene (EH) from 11,700 to 8200 BP; the Middle Holocene (MH) from 8300 to 4200 BP; the Late Holocene (LH) from 4200 to 1850 CE; Historic (Hist) from 1850 to1950 CE; and Modern (Mod) from 1950 CE to the present. Time bins were divided by major ecological, climatic or historical events to represent ecologically relevant periods, and therefore do not necessarily encompass the same amount of time. A taxon was considered present in a temporal community if any part of it’s determined stratigraphic range at Hall’s Cave fell within the time range. Additionally, the modern community includes all mammal species with native geographic ranges encompassing Kerr county with the exception of those with known habitat requirements that did not match the local environment of Hall’s Cave, such as wetland adapted species.

To investigate the role of introduced species, we included five of the most common exotic herbivores found in the vicinity of Hall’s Cave: Blackbuck antelope (Antilope cervicapra), axis deer (Axis axis), sika deer (Cervus nippon), fallow deer (Dama dama) and scimitar‐horned oryx (Oryx dammah). Although all are known to have populations on private ranches, Antilope cervicapraAxis axisCervus nippon and Dama dama also have wild populations on the Edward’s Plateau. In addition to exotic species, we included seven common mammalian livestock and commensal species not otherwise native to central Texas. Trait data for these species was determined using the same methods as previously described.

Usage Notes

The README file contains a description of all variables and additonal usage notes.


National Science Foundation, Award: DGE‐1418062

National Science Foundation, Award: DEB 1555525

National Science Foundation, Award: DEB 1744223