Introduction
Understanding how taxa within a community respond to shared
environmental variation is of particular relevance in the context of
climate change. Climatic changes can affect species distributions,
population abundance, and evolution due to impacts on genetic drift,
structuring of genetic variation, gene flow, and selection (Foden et
al., 2019; Román-Palacios & Wiens, 2020; Aguirre-Liguori et al., 2021).
Species’ responses depend on their ecological niche, defined as all the
variables that influence organismal fitness (Hutchinson, 1957; Blonder,
2018). A species niche will determine the amount and quality of habitat
available to populations, which can change independently. Habitat
quantity has been commonly used as a metric of population abundance as
predicted by metapopulation and island biogeography theory (Fahrig et
al., 2013). However, the amount of habitat is not sufficient to describe
all processes affecting a species and can be misleading, and evidence
suggests that habitat quality should also be considered (Morletilli et
al., 2010; Walting et al., 2020; Galán-Acedo et al., 2021; Regolín et
al., 2021). Separately assessing how habitat availability and habitat
quality changed over past climatic changes for a range of species offers
an opportunity to understand the degree to which these patterns are
coupled, and therefore offer more nuanced information about how
organisms may respond to ongoing and future climate changes.
The ecological niche can be modeled in terms of the climate factors that
determine the occurrence of species in space, or the “Grinnellian
niche” (Soberón, 2007; Sillero et al. 2021). Most studies addressing
the effect of climatic changes on species with a niche modeling approach
focus on habitat quantity and distribution, and relatively fewer studies
have focused on changes in habitat quality (But see Morente-López et
al., 2022; Kebaïli et al., 2023). The ecological niche can be
represented as an ellipsoid in multivariate space, consisting of the
range of suitable conditions for a defined taxon based on a determined
set of variables (Jiménez et al., 2019; Osorio-Olvera et al., 2020a). In
this framework, the ellipsoid centroid (niche centroid) corresponds to
high suitability conditions and high habitat quality, whereas positions
in the multidimensional space near the ellipsoid borders correspond to
more marginal conditions or lower habitat quality (Martínez-Meyer et
al., 2012; Osorio-Olvera et al., 2020b). According to the
center-marginal hypothesis (Eckert et al., 2008; Pironon et al., 2017),
populations living under more suitable conditions present higher
abundance and genetic diversity, whereas populations inhabiting more
marginal conditions are expected to have lower abundance, lower genetic
diversity, and higher drift (Lira-Noriega & Manthey, 2014; San Juan et
al., 2021). Moreover, populations living at the limit of their
tolerances often experience higher selection pressure and respond by
adapting to those challenging environmental conditions (Aguirre-Liguori
et al., 2017, Bontrager et al., 2020). Therefore, a population’s
distance to the ellipsoid centroid may be proportional to selection
pressure.
As climatic conditions change, populations may track suitable
environmental conditions geographically, assuming that niches do not
evolve (i.e., niche conservatism; Wiens et al., 2010). This can result
in changes in the species’ distribution and leave a genomic signature of
range expansion (Lenoir & Svenning, 2015; Tomiolo & Ward, 2018). It
can also lead to founder effects and surfing of deleterious alleles at
the margin of the expanding front (‘allele surfing’; Escoffier et al.,
2008; Gilbert et al., 2018). Further, climate changes can affect species
abundance by the reduction or increase in the amount of suitable area
(Fahrig et al., 2013). Regarding habitat quality, changes in climatic
conditions can affect population fitness and selection pressure because
the distribution of habitats closer to the niche centroid and marginal
conditions could shift. For instance, a geographic location consisting
of conditions matching the niche centroid at one time could shift to
more marginal conditions at a different time, while still being
suitable. Therefore, populations inhabiting this area would experience a
population decline, and/or decrease in fitness and/or an increase in
selection pressure on traits related to variables that have become
marginal at that location. This highlights that environmental changes
can affect both habitat quantity and habitat quality independently and
they yield different population genomic predictions.
The Baja California peninsula (BCP) is a good system to assess how
different taxa respond to changes in habitat quantity and quality during
different climatic conditions. It presents a wide variety of ecosystems
ranging from desert scrub to high-altitude forests (Rebman & Roberts,
2012). It spans 10 degrees of latitude with stark differences in
rainfall and temperature and since it is a peninsula, ecological and
expansion-dispersal dynamics are constrained by its geography (Dolby et
al., 2015). Native species have largely been co-distributed and isolated
from the mainland since the Gulf of California finished flooding 6.3 Mya
(Oskin & Stock, 2003; Darin et al., 2024). In particular, low and high
amplitude glaciation cycles during the Pleistocene (~3
Mya) are expected to have had a large impact on redistributing climatic
conditions and therefore the distribution and abundance of populations
(Dolby et al., 2015). About 80 taxa show a diffuse north-south genetic
co-divergence signal centered in the middle of the Peninsula (Dolby et
al., 2015; Araya-Donoso et al., 2022) and show ecological niche
divergence, suggesting potential adaptation to local environmental
conditions (Cab-Sulub & Álvarez-Castañeda, 2021), which offers an
opportunity to assess both species-level and clade-specific changes in
habitat quantity and quality. It also allows us to test which organismal
features determine responses to environmental change. For example,
highland species that can resist cold may respond differently than
species inhabiting lowland deserts adapted to low water availability, or
taxonomic groups with different physiological requirements, such as
mammals, plants, and reptiles, could also respond specifically.
Previous models and descriptions have detected contrasting patterns of
species distribution to the Last Glacial Maximum (LGM) on the peninsula.
Some taxa show range expansions during LGM (e.g. Graham et al., 2014;
González-Trujillo et al., 2016; Harrington et al., 2017; Arteaga et al.,
2020), whereas others show range contractions (Klimova et al., 2017;
Valdivia-Carrillo et al., 2017). Cab-Sulub & Álvarez-Castañeda (2021)
proposed that southern clades within species contracted their
distribution ranges to LGM, whereas northern clades expanded.
Furthermore, some studies have assessed species’ past demography with
genetic data showing signatures of population contraction towards LGM
(Álvarez-Castañeda & Murphy, 2014; Ferguson et al., 2017; Phuong et
al., 2017; Martínez-Noguez et al. 2020), which does not agree with the
range expansion patterns proposed by some distribution models.
Therefore, changes in population size could be determined by not just
habitat quantity but also habitat quality.
Here, we used ecological niche modeling and species distribution
modeling to compare intra-specific and inter-specific distribution
patterns and niche marginality of 21 taxa from the Baja California
peninsula including mammals, reptiles and plants that inhabit highland
and lowland environments, and have different levels of genetic
divergence along the peninsula. We aimed to assess changes in habitat
quantity and quality between LGM and present day and determine if
organismal characteristics affected these patterns. Then, we used our
models to generate predictions about the effects of historical climate
change on abundance and selection pressure on natural populations that
can be tested in the future with genomic data.