DOI: 10.5061/dryad.w6m905qpv
title: The hidden legacy of megafaunal extinction: loss of functional diversity and resilience over the late Quaternary at Hall’s Cave

description: 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. https://doi.org/10.1111/geb.13428” 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.
description: 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
 log<sub>10</sub>‐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
 log<sub>10</sub>‐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 (<em>Antilope cervicapra</em>), axis deer (<em>Axis axis</em>), sika deer (<em>Cervus nippon</em>), fallow deer (<em>Dama dama</em>) and scimitar‐horned oryx (<em>Oryx dammah</em>). Although all are known to have populations on private ranches, <em>Antilope cervicapra</em>, <em>Axis axis</em>, <em>Cervus nippon</em> and <em>Dama dama</em> 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.
description: The README file contains a
 description of all variables and additonal usage notes.