DOI: 10.5061/dryad.pg4f4qrmw
title: Data for Body mass-related changes in mammal community assembly patterns during the late Quaternary of North America

description: The late Quaternary of North America was marked by prominent ecological
 changes, including the end-Pleistocene megafaunal extinction, the spread
 of human settlements, and the rise of agriculture. Here we examine the
 mechanistic reasons for temporal changes in mammal species association and
 body size during this time period. Building upon the co-occurrence results
 from Lyons et al. (2016) – wherein each species pair was classified as
 spatially aggregated, segregated, or random – we examined body mass
 differences (BMD) between each species pair for each association type and
 time period (Late Pleistocene: 40,000 14C - 11,700 14C ybp, Holocene:
 11,700 14C - 50 ybp, and Modern: 50 - 0 yrs). In the Late Pleistocene and
 Holocene, the BMD of both aggregated and segregated species pairs was
 significantly smaller than the BMD of random pairs. These results are
 consistent with environmental filtering and competition as important
 drivers of community structure in both time periods. Modern assemblages
 showed a breakdown between BMD and co-occurrence patterns: the average BMD
 of aggregated, segregated, and random species pairs did not differ from
 each other. Collectively, these results indicate that the late Quaternary
 mammalian extinctions not only eliminated many large- bodied species but
 were followed by a re-organization of communities that altered patterns of
 species coexistence and associated differences in body size.
description: <i>Dataset</i> We analyzed a dataset of pairwise
 associations produced in Lyons et al. (2016). In this work by Lyons and
 colleagues, species associations were evaluated using species-by-site
 presence-absence matrices from 369 localities across North America. The
 dataset covers three different time periods: Late Pleistocene (40,000
 <sup>14</sup>C ybp to 11,700 <sup>14</sup>C ybp),
 Holocene (11,700 <sup>14</sup>C ybp to 50 ybp) and Modern (50
 – 0 ybp). Lyons et al. (2016) generated this co-occurrence data based on a
 collection of datasets known to include reliable data to minimize bias
 related to taxonomic resolution and taxa misidentification. The studied
 assemblages consisted of lists of species in a locality. Information about
 dataset collection and preparation for the analysis in Lyons et al. (2016)
 is fully detailed in Appendix 1. For each species in Lyons et al.
 (2016), estimates of average body mass in grams were extracted from the
 MOM (Mass of Mammals) database (Smith et al. 2003) version 3. For extant
 species, estimates were averaged across sexes and species’ geographic
 ranges. For extinct mammals, the MOM database compiled body mass estimates
 from the primary and secondary literature, and from regressions using
 tooth measurements. Body mass data were log10-transformed prior to
 analyses. BMDs were then calculated between each pair of North American
 mammal species. While some species’ average body masses might have changed
 through time, our log-transformation makes it unlikely that results would
 be substantially affected; temporal changes in average body mass would
 need to change across an order of magnitude to impact our
 results. <i>Analyses</i>
 <i>PAIRS analyses</i> Lyons et al. (2016) performed the
 original evaluation of pairwise co-occurrence, whose results form the
 basis of our analysis. More details about their analysis can be found in
 Appendix 1, but the general logic of the method will be described here.
 Briefly, to determine whether each pair of species was aggregated,
 segregated, or randomly associated for a given time period, a
 co-occurrence metric (i.e., C-score) was calculated for each pair of
 species in a species-by-site presence-absence matrix. A null distribution
 of C-scores was then generated by shuffling matrix elements, while
 preserving row and column totals (i.e., the “fixed-fixed” algorithm). The
 observed C-score was then compared to the null distribution to determine
 whether a given species pair was significantly aggregated, segregated, or
 random. These analyses were conducted using the software application PAIRS
 version 1.0 (Ulrich 2008). Overall, there were 25,459 species pairs across
 the three time intervals (Late Pleistocene, Holocene and Modern). Table 2
 summarizes the results in Lyons et al. (2016). Previous research (Lyons et
 al. 2016; Tóth et al. 2019) has shown that these types of co-occurrence
 analyses are robust to differences in collection mode, temporal grain,
 spatial or temporal extent, taphonomic bias, taxonomic resolution, and
 sampling biases. Lyons, S. K.,
 K. L. Amatangelo, A. K. Behrensmeyer, A. Bercovici, J. L. Blois, M. Davis,
 W. A. DiMichele, A. Du, J. T. Eronen, J. Tyler Faith, G. R. Graves, N.
 Jud, C. Labandeira, C. V. Looy, B. McGill, J. H. Miller, D. Patterson, S.
 Pineda-Munoz, R. Potts, B. Riddle, R. Terry, A. Tóth, W. Ulrich, A.
 Villaseñor, S. Wing, H. Anderson, J. Anderson, D. Waller, and N. J.
 Gotelli. 2016. Holocene shifts in the assembly of plant and animal
 communities implicate human impacts. Nature
 <b>529</b>:80-83. Smith, F. A.,
 S. K. Lyons, S. K. M. Ernest, K. E. Jones, D. M. Kaufman, T. Dayan, P. A.
 Marquet, J. H. Brown, and J. P. Haskell. 2003. Body mass of late
 Quaternary mammals. Ecology 84:3403-3403. Ulrich, W.
 2008. Pairs—a FORTRAN program for studying pair-wise species associations
 in ecological matrices. Version 1.0. http://www.keib.umk.pl/pairs/?lang=en.
description: <strong>allData file:</strong>
 Sp1: Species 1 in a pair of species Sp2:
 Spacies 2 in a pair of species Pleistocene: 1 species
 pair exists in this time period; 0 species pair does not exist in this
 time period Holocene: 1 species pair exists in this
 time period; 0 species pair does not exist in this time period
 Modern: 1 species pair exists in this time period; 0 species pair
 does not exist in this time period PleisPairType:
 Association type for this species pair in the Late Pleistocene
 HoloPairType: Association type for this species pair in the
 Holocene ModPairType: Association type for this species
 pair in the Modern BM_gSp1: Body mass in grams of
 species 1 in a species pair BM_gSp2: Body mass in grams
 of species 2 in a species pair
 <strong>Localities_Pineda-Munoz
 file:</strong> Time: Locality time (Pleistocene,
 Holocene or Modern) Locality: Locality name of
 fossil/modern locallity TimeYbp: Locality time in
 ybp Lat: Latitude of the locality (WGS 1984)
 Long: Longitude of the locality (WGS 1984)
 Durantion: Time span of the locality (applicable to fossil
 localities) spaceExtent: Spatial extent represented by
 the locality in squared kilometers