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ECOGRAPHY

Research article

Global phylogenetic and functional structure of
rodent assemblages

Yoan Fourcade ID^1^ and Bader H. Alhajeri ID^2

**Correspondence: Yoan Fourcade (yoan.fourcade@u-pec.fr)**

Ecography

2025: e07534

doi: 10.1002/ecog.07534

Subject Editor: Pedro Peres-Neto

Editor-in-Chief: Miguel Araújo

Accepted 13 March 2025

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Exploring the global patterns of phylogenetic and functional structure of assemblages is key to describe the distribution of biodiversity on Earth and to predict how communities and ecosystem functioning may be affected by anthropogenic pressures. Rodent communities have been studied in this regard in the past, but previous work largely focused on desert ecosystems. Here, we leveraged a large database of rodent range maps, functional traits, and phylogenetic trees to compute several metrics of functional and phylogenetic structure across > 10 000 rodent assemblages spanning all terrestrial biomes. We found that the vast majority of assemblages did not significantly differ from random association among species. Importantly, we show that the current patterns we observed can locally differ from past community structure, revealing the role humans have played in altering large-scale biodiversity patterns. We also showed a strong scale-dependence of our metrics and revealed a weak correlation between phylogenetic and functional structure, providing an additional line of evidence that they do not reflect the same processes of community assembly.

Keywords: clustering, community assembly, community structure, overdispersion,
species pool

Introduction

Understanding the structure of species assemblages and the rules behind community
assembly represents a common challenge for ecologists interested in the distribution
of biodiversity on Earth or in the factors driving the provision of ecosystem services
(Ricklefs 2004, Dehling et al. 2022). A way to advance our knowledge of these pat-
terns is to build upon the observation of current assemblages and to describe their
diversity in relation to the degree of (dis)similarity of species (Pavoine and Bonsall
2011, Safi et al. 2011). Under certain circumstances, communities are expected to be
composed of species sharing similar functional traits, for example because environ-
mental conditions have selected for the same set of traits (habitat filtering). On the

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<footnote n="1">¹Univ Paris Est Creteil, Sorbonne Université, Université Paris-Cité, CNRS, IRD, INRAE, Institute of Ecology and Environnemental Sciences, IEES, Créteil, France</footnote>

<footnote n="2">²Department of Biological Sciences, Kuwait University, Safat, Kuwait, Kuwait</footnote>
other hand, strong competitive pressure may act as a selective
filter leading to communities composed of divergent species
because of competitive exclusion of species sharing a similar
niche (Webb et al. 2002, Kraft et al. 2015).

While community assembly rules are expected to act on
species' functional traits, it is difficult to collect all the traits
that drive the structure of a given community (Etard et al.
2020). Therefore, under the hypothesis that trait diversity
emerges from evolutionary processes (Freckleton et al. 2002),
the phylogenetic diversity of communities – i.e. the amount
of evolutionary history accumulated by the set of species
in a community – is hypothesised to be a good proxy for
their functional diversity (Webb et al. 2002). However, it has
become clear that functional and phylogenetic diversity do
not necessarily coincide (Devictor et al. 2010, Mazel et al.
2018, Ramm et al. 2018). This can be due to convergent evo-
lution, making distantly related species similar in terms of the
traits they harbour (Starko et al. 2020). Habitat filtering may
also select for different levels of phenotypic variation within
a clade depending, e.g. on habitat heterogeneity, hence blur-
ring the correlation between functional and phylogenetic
diversity (Devictor et al. 2010). It makes them two comple-
mentary measures of community diversity and structure,
deserving attention for different purposes (E-Vojtkó et al.
2023). While the functional structure of communities may
be important for understanding how they formed and how
they determine ecosystem properties, phylogenetic structure
represents an important feature for interpreting the evolu-
tionary history and potential of species assemblages (Faith
1992, Winter et al. 2012).

To distinguish between communities that are composed
of related/similar species and those of species that are func-
tionally or evolutionarily distinct, it is necessary to estimate
how much diversity there is within a community compared
to what is expected randomly for a given species richness
(Webb 2000, Webb et al. 2002). This is generally performed
by randomising community composition from a species pool
in order to produce a null distribution of functional or phy-
logenetic diversity metrics, to which the observed metrics
of diversity are compared (Kembel et al. 2010, Miller et al.
2017). In theory, the true species pool is the set of species
that would be able to reach the focal site given their dispersal
ability (Zobel 2016). However, in global scale studies where
assemblages are considered at broad scale and not from direct
field sampling, one must decide the spatial extent that con-
stitutes the potential source of species that supports commu-
nity assembly (Cornell and Harrison 2014). Exploring how
functional and phylogenetic community structure vary with
different species pools may improve our comprehension of
scale-dependent processes of community assembly.

Community assembly rules and assemblage structure have
been studied for a while in rodents (M'Closkey 1976), which
are present in all continents and biomes, and constitute the
most diverse mammal taxon. Specifically, there is a large body
of work concerning rodent community structure in desert
ecosystems (Bowers and Brown 1982, Brown et al. 2000,
Stevens et al. 2012, Shenbrot 2014, Alhajeri and Steppan

2018, Christensen et al. 2018). Evidence from early stud-
ies indicated that competition plays a large role in shaping
rodent communities in North American deserts (Bowers
and Brown 1982, Brown and Munger 1985), although it
appeared that patterns were complex and could not be gen-
eralised everywhere (Shenbrot et al. 1999). Discrepancies
between studies may be due to different traits (morpho-
logical, dietary or locomotion traits) reflecting different
mechanisms. Some traits can be linked to processes of spe-
cies coexistence while others can be selected by environmen-
tal filtering. In this regard, a recent study conducted in 15
desert ecosystems across all continents revealed that rodent
assemblages were mostly randomly assembled, both in terms
of phylogeny and morphological traits (Alhajeri and Steppan
2018). The growing availability of large-scale distributional
data, coupled with recent compilations of functional traits
and phylogenies spanning nearly all rodent species, makes it
now possible to advance beyond these previous studies and to
investigate rodent community structure globally and across
all ecosystems.

In the present study, we leveraged a large database of rodent
range maps (IUCN 2024), functional traits (Wilman et al.
2014, Alhajeri et al. 2020, Soria et al. 2021, Fourcade and
Alhajeri 2023) and phylogenetic trees (Upham et al. 2019)
to compute several metrics of functional and phylogenetic
structure across > 10 000 rodent assemblages spanning all
terrestrial biomes. We conducted null model computations,
considering ecoregions as the scale of the species pool, to
estimate which assemblages are non-randomly structured
(and in which direction). Because we assumed that observed
community structure may be influenced by human-driven
introduction or extirpation of species, we compared current
patterns with historical community structure inferred from
past species ranges. We also tested the effect of considering
species pools at a much larger spatial scale: biogeographic
realms. We described congruence and discrepancies between
functional and phylogenetic structure. Finally, we related
community structure metrics to climate variables and to
assemblage-level species richness to characterise the role that
environmental filtering and competition could have played
in shaping rodent assemblages globally. Our results provide
significant advances to understanding assembly rules across
all types of ecosystems in rodents, which is one of the most
studied taxonomic groups in ecology.

**Material and methods**

Data collection

We obtained distributional data for nearly all described rodent
species (n=2276) from the most up-to-date range maps pro-
duced by the International Union for Conservation of Nature
(downloaded in October 2024). While these maps are too
coarse to determine which species interact with each other at
small scales (Higino et al. 2023), they still provide the most
up-to-date information regarding the global distribution of
rodents, and have been successfully used in previous macroecological studies to characterize species assemblages (Maréchaux et al. 2017, Alhajeri et al. 2020, Fourcade and Alhajeri 2023). We distinguished two types of distributional data: the current range of species, for which we selected all areas where species are classified as extant, and the historical range of species characterised by the areas where species are either extant or extinct, excluding areas of introduction. Since these datasets were more recent than the phylogenetic trees and trait data described below, we matched synonyms using the 'PhyloMatcher' software (Rader et al. 2023) and the 'rredlist' R package (Chamberlain 2020).

Phylogenetic relatedness was estimated from a random subset of 200 trees extracted from the mammal phylogenetic trees of Upham et al. (2019). We sampled 100 trees based on genetic information (1466 species), and 100 'completed' trees (2170 species) that were imputed with species missing DNA data.

We compiled species traits from different sources (Supporting information). First, we used the COMBINE database of mammal intrinsic and extrinsic traits, which originally contains information on 54 traits for 2427 species, using phylogenetic imputation for missing data (Soria et al. 2021). We complemented this data source with various species traits already compiled and used in Alhajeri et al. (2020) and Fourcade and Alhajeri (2023). It included morphological measurements extracted from museum databases and literature, range size extracted from IUCN range maps, mean climatic conditions encountered by species obtained by intersecting range maps and climate data, and habitat type obtained from the IUCN Red List assessments, as well as species life mode from the EltonTrait database (Wilman et al. 2014). We retained only traits with < 5% missing species, resulting in a final database comprising 27 traits covering 2257 species, among which 1695 had information for all the 27 traits. We found that 517 species had trait data but were not present in the phylogenetic trees (Supporting information). We intended to collect a maximum number of traits to get a broad overview of the functional structure of rodent assemblages, but since different traits represent different ecological processes of community assembly, we analysed them together first, then separately in four distinct groups: 1) diet (1760 species): proportion of invertebrates, vertebrates, and plants in each species' diet, diet breadth, foraging stratum, and trophic level; 2) reproduction (1786 species): female maturity, age at first reproduction, gestation length, litter size, number of litters per year, interbirth interval, weaning age, and generation length; 3) morphology (2205 species): tail length, hind-foot length, and head-to-body length; and 4) habitat (2106 species): main habitat type, habitat breadth, range size, life mode (i.e. terrestrial, arboreal, scansorial, or subterranean), as well as the mean value of six climate variables across species' range - mean annual temperature (bio 1), maximum temperature of the warmest month (bio 5), minimum temperature of the coldest month (bio 6), annual precipitation (bio 12), precipitation of wettest month (bio 13), and precipitation of driest month (bio 14). Each of these trait

categories represents a different aspect of the niche of species, allowing us to interpret more easily the patterns of functional structure and their potential drivers.

To define regional species pools, we used the map of ecoregions produced in the Ecoregions 2017 project (Dinerstein et al. 2017), an update of the Terrestrial Ecoregions of the World previously compiled by the World Wildlife Fund (Olson et al. 2001). It defines 846 ecoregions that represent areas sharing similar environmental features and relatively homogeneous biological communities. The ecoregions are nested within 14 biome types (including desert, forest, and grassland biomes) and eight biogeographical realms.

Finally, we obtained climate data from the CHELSA database (Karger et al. 2017, 2018), as potential correlates of community structure. Specifically, we downloaded rasters at a resolution of 30' for the following variables, depicting the global variation in temperature and precipitation conditions: mean annual temperature (MAT, bio 1) and annual precipitation (AP, bio 12).

## Phylogenetic and functional structure

We defined assemblages as point locations chosen following a random sampling stratified by biomes, with an approximately similar number of locations per biome (mean=996, Supporting information), ranging from 913 (montane grasslands and shrublands) to 1070 (mangroves). We overlapped these points with the range maps of rodent species to define the composition of rodent assemblages in each of these locations (13 942 assemblages in total). Overall, the rodent assemblages we defined following this approach contained between 1 and 51 (current ranges) or 50 (historical ranges) species (Supporting information). After removing locations with a single species, the final dataset was reduced to 13 464 (current ranges) or 13 323 (historical ranges) assemblages. Since some narrow-ranged species did not overlap the sampled locations, the assemblages we analysed comprised only 1794 species.

In each rodent assemblage, we calculated measures of community structure, computed using both 'DNA-based' and 'completed' phylogenetic trees as measures of phylogenetic relatedness. We selected two commonly used metrics: the mean nearest taxon distances (MNTD), and the mean pairwise distances (MPD). Although they both measure phylogenetic diversity within an assemblage, MPD is influenced by phylogenetic relatedness between distantly related taxa, while MNTD is only driven by recent speciation events (Webb 2000). Our assessment of the phylogenetic structure of rodent assemblages was based on whether our measures of phylogenetic diversity were higher or lower than expected by chance, given the set of species present in each assemblage and the available species pool. This was done by calculating a standardized effect size of MNTD and MPD using the 'phylogeny pool' randomization algorithm implemented in the 'picante' R package (Kembel et al. 2010). The resulting standardized metrics (referred to as SES MNTD and SES MPD from now on) were > 0 for assemblages that
were phylogenetically over-dispersed compared to random expectations and < 0 for assemblages that were phylogenetically clustered. We also computed p-values – again using the comparison between observed and randomised values – to determine which assemblages were significantly (at α=0.05) over-dispersed or clustered. All analyses were repeated for 100 DNA-based and 100 completed trees, and we reported the mean values obtained over 200 results.

For each assemblage, we also computed measures of func-
tional structure, first using the species for which we had data
for all 27 traits. For these measures to be easily comparable
with our estimates of phylogenetic structure, we used exactly
the same procedure, using a matrix of functional distances
instead of phylogenetic distances derived from phylogenetic
trees. Pairwise functional distances were computed as the
Gower's distance between species, which can handle both
continuous and discrete trait values (Gower 1971). We pro-
duced estimates of functional SES MNTD and SES MPD,
and their associated p-values, to map assemblages that were
functionally over-dispersed or clustered. To distinguish
between different types of traits, we repeated the calculations
for each trait type separately (diet, reproduction, morphol-
ogy, and habitat). Gower's distances were computed using the
'cluster' R package (Maechler et al. 2022).

Our main analyses considered as species pool, for each assemblage, the set of species present in the same ecoregion. However, because measures of functional and phylogenetic structure may be scale-dependent (Jarzyna and Jetz 2018), we repeated the above analyses defining species pools at a larger scale, being composed of the species belonging to the same biogeographical realm. Therefore, a total of 48 analyses of community structure was performed for each assemblage: two indices (SES MNTD and SES MPD) × six types of structure (phylogenetic, functional [all traits + each of the five trait categories separately]) × two time periods (current ranges and historical ranges) × two spatial scales (ecoregions and realms).

Statistical analyses

We reported estimates of Pearson's correlation (r coefficient
and p-values) between functional and phylogenetic structure,
between results obtained using either current or historical
ranges of rodent species, and considering ecoregion or realm
as the species pool. In addition, we mapped the significant
metrics of functional and phylogenetic structure to highlight
regions that are clustered or over-dispersed in one or both.

We also tested if phylogenetic and functional structure of
rodent assemblages were related to environmental features.
In addition to environmental filtering, biotic interactions
may also contribute to community structuring. Therefore,
we assumed that the diversity of assemblages can reflect com-
petition intensity, and thus be potentially positively associ-
ated with our measures of community structure (i.e. more
dispersion in the richest assemblages). We built linear mixed
models to analyse variations in phylogenetic and functional
structure as a function of species richness and two climate

variables (mean annual temperature [MAT] and annual pre-
cipitation [AP]) as descriptors of global-scale natural variation
in environmental conditions. In each model, we included
ecoregion nested within biome nested within realm as ran-
dom intercept to control for spatial autocorrelation. Since the
effects of temperature and precipitation may be non-linear,
we implemented models with either: 1) both temperature
and precipitation as second-order polynomials (i.e. quadratic
relationships), or 2) only one of them as a second-order poly-
nomial, or 3) both linear. We selected among those models
– along with a null intercept-only model – the one with the
lowest Akaike information criterion corrected for small sam-
ple sizes (AICc, *Burnham and Anderson 2002*).

Results

Phylogenetic structure

Rodent assemblages had a mean phylogenetic SES MNTD of 0.174 and a mean phylogenetic SES MPD of -0.089. Among all assemblages, 5.7 and 8.5% were significantly phylogenetically clustered in terms of SES MNTD and SES MPD, respectively, while 9.4% (SES MNTD) and 6.3% (SES MPD) were phylogenetically over-dispersed (Fig. 1). Although it was difficult to distinguish a clear geographical pattern, the spatial distribution of SES MNTD and SES MPD values (Fig. 1A) was not random, as we observed areas of contiguous overdispersed or clustered assemblages. There was no strong difference between biomes or between biome types, being all mostly non-significantly structured (Fig. 1B).

Overall, results from historical species ranges did not vary
much from those generated based on their current distribu-
tions (Pearson's correlation; SES MNTD: *r* = 0.92, *p* < 0.001;
SES MPD: *r* = 0.95, *p* < 0.001). However, we observed some
regional trends such as Australia, North America, and coastal
regions of South America that appeared to have greater phy-
logenetic over-dispersal today than in the past (increased SES
MNTD and SES MPD). In contrast, Europe (SES MNTD
and SES MPD) and Eastern Asia (SES MPD only) showed
greater clustering (Supporting information).

Phylogenetic structure estimated from recent phylogenetic
relationships (SES MNTD) or from deep evolutionary rela-
tionship (SES MPD) were only weakly, albeit significantly,
correlated (r = 0.48, p < 0.001; Supporting information).
Estimates obtained using biogeographical realms as species
pools were relatively strongly correlated with those obtained
from ecoregions (SES MNTD: r = 0.72, p < 0.001; SES
MPD: r = 0.71, p < 0.001; Supporting information).

Functional structure

The functional structure of rodent assemblages – consider-
ing all traits – was characterised by a mean SES MNTD of
–0.445 and a mean SES MPD of –0.352. Around 13% of
all assemblages were functionally clustered (SES MNTD:
<figure><img src="image_4.png" /><figcaption>Figure 1. Phylogenetic structure of rodent assemblages, using current range of species and ecoregions as species pools. (A) Map of the values of standardized effect size of mean nearest taxon distances (SES MNTD) and SES of mean pairwise distances (SES MPD) obtained in the 13 464 assemblages. (B) Proportion of assemblages that are significantly (p-value < 0.05) clustered or over-dispersed in each biome, grouped into desert, forest, and grassland biomes.</figcaption></figure>

13.6%, SES MPD: 13.2%), more than three times the pro-
portion of over-dispersed assemblages (SES MNTD: 3.8%,
SES MPD: 4.3%) (Fig. 2). Similar to our results for phyloge-
netic structure, we observed little difference between biome
types overall, as they were all dominated by non-significant
structure (Fig. 2B). Looking at habitat traits, it appeared that
assemblages were particularly strongly clustered (mean SES
MNTD<sub>habitat</sub> = -0.675, 22.1% significantly clustered, mean
SES MPD<sub>habitat</sub> = -0.921, 29.4% significantly clustered)
(Fig. 2C-D). In contrast, the reproductive traits showed a
general signal of overdispersion, especially when measured
with SES MNTD, with 10.2% of assemblages that were
significantly over-dispersed while only 4.7% of assemblages
were clustered (Fig. 2C).

The historical and current ranges of species led to strongly
correlated estimates of functional structure (r = 0.92, p <
0.001 for both SES MNTD and SES MPD). Here as well,
changes were not uniform: we observed that Australia, for
example, has become more overdispersed (SES MNTD and
SES MPD have increased in current conditions compared to
past ranges), while some regions in Europe, Eastern Asia, the
central part of South America, and boreal areas appeared to
have faced a decrease in our measures of functional structure;
i.e. they became more clustered than they were in the past
(Supporting information).

Both metrics of functional structure were strongly cor-
related (r = 0.84, p < 0.001; Supporting information).
However, metrics of functional structure calculated from
biogeographical realms were only weakly correlated with the
values obtained from ecoregions (all traits, SES MNTD: r =
0.65, p < 0.001; SES MPD: r = 0.64, p < 0.001). The cor-
relation was particularly low, even if it remained significant,
for the habitat and diet traits when functional structure was
assessed using the SES MPD index (habitat: r = 0.52, p <
0.001; diet: r = 0.55, p < 0.001; Supporting information).

Difference between phylogenetic and functional
structure

Metrics of phylogenetic and functional structure were sig-
nificantly, but weakly correlated (SES MNTD: *r*=0.42, *p*
< 0.001; SES MPD: *r*=0.55; Fig. 3B). Assemblages that
were both phylogenetically and functionally structured in the
same way (clustered or over-dispersed) were rare. Assemblages
where phylogenetic and functional structure were reversed
were even rarer; in particular, there was not a single assem-
blage that was phylogenetically clustered but functionally
overdispersed (Fig. 3A). There were, however, large contigu-
ous regions characterised by a functional structure that did
not differ from random, but had a significantly overdispersed
phylogenetic structure (in dark red in Fig. 3A; e.g. across
North and South America for SES MPD). An even larger
area featured a phylogenetic structure that did not differ from
random but had a significantly clustered functional structure
(in dark green in Fig. 3A; e.g. for SES MPD: Siberia and
South-Eastern Asia).

Drivers of community structure

All selected models included species richness and a qua-
dratic effect of both MAT and AP as predictors of commu-
nity structure. In all cases except for functional SES MNTD
computed with morphological traits only, the second-best
model featured a ΔAICc > 16 compared to the best-fitting
model (Supporting information). Phylogenetic SES MNTD
and SES MPD were highest in assemblages characterised
by a MAT of approximately 15°C, and at low values of AP.
Functional SES MNTD and SES MPD tended to peak at
intermediate values of MAT and AP, although the relation-
ship could be slightly different for functional metrics calcu-
lated for specific trait types (especially reproduction and diet
<figure><img src="image_5.png" /><figcaption>Figure 2. Functional structure of rodent assemblages, using current range of species and ecoregions as species pools. (A) Map of the values of SES MNTD and SES MPD obtained in the 13 464 assemblages, all traits considered. (B) Proportion of assemblages that are significantly clustered or over-dispersed in each biome, grouped into desert, forest, and grassland biomes, all traits considered. (C)–(D) As in (A) and (B), for each of the four trait types separately.</figcaption></figure>

traits). There was a positive association between phylogenetic SES MNTD and SES MPD, and species richness. Functional SES MNTD and SES MPD measured from all traits or from habitat traits only were negatively associated with species richness. However, the effect of species richness was positive for functional structure measured from diet traits only, and was non-significant for reproduction traits (Fig. 4, Supporting information).

## Discussion

The study of rodent communities has a long tradition rooted in early work focused on desert ecosystems (Bowers and Brown 1982, Brown et al. 2000, Stevens et al. 2012, Shenbrot 2014, Alhajeri and Steppan 2018, Christensen et al. 2018). Here, we considerably extend this previous knowledge by investigating the structure of rodent assemblages on a global
<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /><figcaption>Figure 3. Relationship between measures of phylogenetic and functional structure of rodent assemblages. (A) Maps showing the assemblages that were significantly clustered in terms of phylogenetic and/or functional structure, for SES MNTD (top) and SES MPD (bottom). (B) Scatterplots of SES MNTD and SES MPD as measures of functional (y-axis) or phylogenetic structure (x-axis). The grey dashed lines represent the 1:1 relationship. Both plots show measures of community structure computed using current range of species and ecoregions as species pools. Measures of functional structure shown in these plots were computed using all traits.</figcaption></figure>

scale, covering all biome types and focusing our attention on both functional and phylogenetic structure. Although there was no single answer to the question of rodent community structure, we nevertheless demonstrated that the vast majority of rodent assemblages were not significantly different from a random association between species, with a very small proportion of clustered or overdispersed assemblages, either phylogenetically of functionally.

Despite an overall lack of structure, some assemblages did show evidence of significant structure, either functional or phylogenetic, positive or negative. Overall, many more

assemblages harboured functional clustering than over-dispersion. This is the case, e.g. in tundra ecosystems where up to 28% of assemblages (using SES MPD) were clustered in terms of functional structure. Community clustering is thought to reveal the influence of environmental variables that only allow the establishment of species featuring certain (adaptive) traits, resulting in assemblages characterised by closely related and/or functionally similar species (Webb et al. 2002, Kraft et al. 2015). A plausible hypothesize is that tundra rodent communities are structured along gradients of moisture, temperature, and vegetation cover (Batzli and Lesieutre

<figure><img src="image_8.png" /><figcaption>Figure 4. Regression lines showing the relationship between measures of phylogenetic (A) or functional (B) structure and three explanatory variables: species richness (i.e. number of species in assemblages), mean annual temperature (MAT), and annual precipitation (AP). Significant relationships are displayed as plain lines while dashed lines show non-significant relationships at the α = 0.05 level.</figcaption></figure>
1995, Ravkin et al. 2009), and are less prone to interspecific competition due to their broad dietary niche (Soininen et al. 2013) and the top-down control of their populations (Ims and Fuglei 2005). Overall, habitat traits appeared to drive the trend towards more frequent functional clustering than overdispersion of traits, which is consistent given our definition of habitat traits that are partly based on species' geographical location. Moreover, we observe a tendency for assemblages in North America to be more frequently phylogenetically overdispersed than elsewhere. Such a pattern has been observed before and has been attributed to an effect of interspecific competition that prevents similar species from coexisting in the same habitat (Bowers and Brown 1982, Brown et al. 2000).

The positive correlation between both measures of phylogenetic structure and the richness of assemblages may suggest a role of interspecific competition, i.e. a stronger competition is a driving force leading to a selection of phylogenetically distant species that have particularly divergent traits (Webb et al. 2002, Kraft et al. 2015). For instance, greater variation in diet preferences, i.e. niche partitioning, is a common pattern allowing species coexistence in highly competitive communities (Brown and Wilson 1956, Hogstad 1978, De León et al. 2014). Accordingly, we found that higher values of functional SES MNTD or SES MPD calculated on diet traits were associated with assemblages harbouring higher species richness. In contrast, SES MNTD or SES MPD calculated on habitat traits were negatively associated with species richness, which is probably a consequence of our measures of habitat traits that are inherently spatially clustered, allowing for greater clumping of similar species in the most diverse assemblages.

The effect of climate on community structure appeared to be non-linear, both phylogenetic and functional SES MNTD or SES MPD being maximal at intermediate temperatures, roughly corresponding to temperate climates. This is consistent with a strong environmental filter that would select a reduced set of species in harsh climatic conditions (cold and warm), as observed in, for example, North American angiosperms (Qian and Sandel 2017). However, it runs counter to the hypothesis of stronger biotic interactions in the tropics, which has been verified for many processes (Schemske et al. 2009), and that should result in functional and phylogenetic overdispersion at high temperature. In this respect, diet niche partitioning has indeed been observed at smaller scales in several rodent communities of tropical forests (Galetti et al. 2016, Crowley et al. 2018). Our results may instead reflect a process of niche packing in the tropics, in which species-rich assemblages exhibit phylogenetic or functional clustering because they are composed of many species sharing the same niche volume (Pigot et al. 2016). We detected an effect of precipitation on functional structure that is mostly similar to that of temperature, with stronger clustering at intermediate values. Phylogenetic SES MNTD, though, appeared to be lowest (i.e. phylogenetic overdispersion is maximal) in regions of highest precipitations, which could be related to stronger interspecific competition in the tropics.

Human activity has shaped species' distributions for a long time (Faurby and Svenning 2015), resulting in current patterns of global assemblages that are influenced by introductions of species far from their native ranges and by local extirpations that have occurred from direct or indirect anthropogenic pressures. As a consequence, it may be difficult to estimate natural macroecological patterns from present-day species occurrence, for example when species' niches are truncated (Sales et al. 2022). Here, we showed that historical community structure, i.e. defined using native ranges only, including regions from which species have now gone extinct, may have differed from current community structure, especially in some specific regions. This is a notable pattern in Australia, in which assemblages have become more dispersed, likely because of the introduction of several European rodent species that are phylogenetically and functionally different from the native rodent fauna (Biancolini et al. 2021). On the other hand, some regions, mostly in Asia and Europe, have become more clustered. This can possibly be attributed to the loss of the diversity of specialist species in favour of a few closely related generalists, a pattern that is commonly observed with global changes (Clavel et al. 2011).

Similar to other evidence that pointed in this direction (Mazel et al. 2018, Jarzyna et al. 2021), our results showed that phylogenetic structure was a poor predictor of the functional structure of communities. Admittedly, both are statistically correlated, but this correlation remained weak and congruence between them was rare. Although phylogenetic diversity has been largely analysed in the past to reflect community assembly processes linked to species' traits, assuming that phylogenetic distance correlates with trait divergence (Webb et al. 2002), we demonstrated here that they may differ strongly (although for both phylogenetic and functional structure, we conclude that most assemblages did not differ from random). Of course, this result may be due to the set of species traits we retained in this study – here we aimed to compile as many traits as possible. Moreover, this result does not stop community phylogeny from being interesting on its own, for example to describe the relationship between species coexistence and diversification (Mazel et al. 2018) or for the purpose of preserving evolutionary history with species assemblages (Winter et al. 2012).

The indices of community structure we calculated in this study differed depending on the species pool considered, especially for functional structure and even more strongly for some traits such as habitat. Specifically, we observed more functional clustering as we enlarged the species pool from which randomisations were carried out. It is reasonable to assume that a local assemblage tends to look particularly homogeneous compared to the set of species present in a whole biogeographical realm (Cornell and Harrison 2014). It sheds light on a key aspect of community structure studies: different hypotheses for delineating species pools could lead to strong variation in the conclusions drawn about community assembly rules. Although we considered here only two spatial scales for defining species pools, alternative approaches can proceed by filtering species based on their
affinity for certain habitat types or based on their dispersal
ability (Cornell and Harrison 2014, Zobel 2016). Another
scale dependence to consider concerns the baseline species
data that are used to define assemblages. While our approach
based on range maps has been used before (Alhajeri and
Steppan 2018, Jarzyna et al. 2021), it remains unable to
characterise communities of interacting species at very local
scales, although this may be necessary for describing true
patterns of interspecific competition. We also showed that
both metrics of diversity and structure that we used could
give rise to slightly different patterns. This is partly expected
since MPD describes deep relatedness between species, while
MNTD reveals relatedness near the branch tips (Kellar et al.
2015). According to our results, rodent assemblages were
on average composed of species belonging to closely related
deep lineages (mean SES MPD < 0, i.e. phylogenetic cluster-
ing) while rodent species tended to co-occur less frequently
than expected with their nearest relatives (mean SES MNTD
> 0, i.e. phylogenetic overdispersion). Although these pat-
terns should not be overinterpreted due the vast majority of
assemblages being indistinguishable from random associa-
tions, it emphasizes another uncertainty in community struc-
ture studies, especially knowing that many more metrics of
phylogenetic and functional structure exist, as well as many
approaches for randomising null communities (Kembel et al.
2010, Kellar et al. 2015, Miller et al. 2017). Moreover, as the
indices we used here were developed for describing phyloge-
netic diversity within assemblages, more research is needed
to understand how they behave and differ as descriptors of
functional structure.

We described in this study the phylogenetic and func-
tional structure of rodent assemblages at an unprecedented
scale. Although our analyses based on range maps cannot
replace field observations of actual communities, we were
able to show using range maps that there was a clear tendency
towards assemblages that did not differ from random associa-
tions between species, at least at the scale of analyses consid-
ered here and considering the set of traits we used. Looking
more specifically at some traits, we detected potential signa-
tures of environmental filtering and interspecific interactions.
Overall, both processes may act in opposite directions, result-
ing in assemblages that appear no different from random on
average. Structure may be further obscured by the role of
additional factors such as elevation (Jarzyna et al. 2021) or
resource heterogeneity (Stevens et al. 2012) that we did not
consider here. We also showed that human disturbance has
contributed to the current patterns of community structure.
In addition to rodent-specific results, our study highlights the
importance of carefully considering the uncertainties associ-
ated with spatial scale and metrics before drawing conclu-
sions and provides another line of evidence that phylogenetic
and functional structure do not necessarily reflect the same
processes of community assembly.

*Acknowledgements* – We thank all the many persons who contributed to gather the data we used, without which such a study would not

have been possible. They include the experts who produced rodent
range maps, the authors of the trait databases, Natham Upham and
his collaborators for the phylogeny, and the curators of museum
specimens from which morphological measurements were taken.

Author contributions

**Yoen Fourcade:** Conceptualization (equal); Data curation (equal); Formal analysis (lead); Methodology (equal); Writing – original draft (lead); Writing – review and editing (equal). **Bader H. Alhajeri:** Conceptualization (equal); Data curation (equal); Methodology (equal); Writing – review and editing (equal).

Transparent peer review

The peer review history for this article is available at https://www.webofscience.com/api/gateway/wos/peer-review/10.1111/ecog.07534.

Data availability statement

All data for this project (location and composition of assem-
blages, traits, phylogenetic trees) are available from the
Figshare Digital Repository: https://doi.org/10.6084/m9 fig
share.25262746.v2 (Fourcade and Alhajeri 2025).

Supporting information

The Supporting information associated with this article is
available with the online version.

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