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Data for Body mass-related changes in mammal community assembly patterns during the late Quaternary of North America

Cite this dataset

Pineda-Munoz, Silvia (2020). Data for Body mass-related changes in mammal community assembly patterns during the late Quaternary of North America [Dataset]. Dryad.


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.



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 14C ybp to 11,700 14C ybp), Holocene (11,700 14C 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.


PAIRS analyses

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 529:80-83.

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.

Usage notes

allData file:

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

Localities_Pineda-Munoz file:

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