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\begin{document}

\title{Habitat quality or quantity? Changes in niche marginality across 21
species of plant and animal suggest differential responses between
highland and lowland species to past climatic changes}



\author[1]{Raúl Araya-Donoso}%
\author[2]{Austin Biddy}%
\author[3]{Adrian Munguía-Vega}%
\author[4]{Andrés Lira-Noriega}%
\author[2]{Greer Dolby}%
\affil[1]{Arizona State University}%
\affil[2]{The University of Alabama at Birmingham College of Arts and Sciences}%
\affil[3]{University of Arizona}%
\affil[4]{Instituto de Ecología AC}%


\vspace{-1em}



  
  \date{May 22, 2024}


\begingroup
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\selectlanguage{english}
\begin{abstract}
Climatic changes can affect species distributions, population abundance,
and evolution. Such organismal responses could be determined by the
amount and quality of available habitats, which can vary independently.
In this study, we assessed changes in habitat quantity and quality
independently to generate explicit predictions of the species' responses
since the Last Glacial Maximum (LGM) climatic changes. We built
ecological niche models and distribution models for 21 reptile, mammal,
and plant taxa from the Baja California peninsula inhabiting lowland or
highland environments. Geological data suggests the CCSM global
circulation model is a better representation of LGM climate for the Baja
California peninsula. Significant niche divergence was detected for all
clades within species, along with significant differences in niche
breadth and area of distribution between northern and southern clades.
Most clades showed a reduction in distribution area towards LGM.
Further, niche marginality (used as a measure of habitat quality) was
higher during LGM for most clades, except for northern highland species
who experienced improvements in both. Our results suggest that changes
in habitat quantity and quality can affect organismal response
independently. This allows the prediction of genomic signatures
associated with changes in effective population size and selection
pressure that could be explicitly tested to support our models.%
\end{abstract}%



\sloppy


\textbf{Habitat quality or quantity? Niche marginality across 21 plants
and animals suggests differential responses between highland and lowland
species to past climatic changes}

\textbf{Abstract}

Climatic changes can affect species distributions, population abundance,
and evolution. Such organismal responses could be determined by the
amount and quality of available habitats, which can vary independently.
In this study, we assessed changes in habitat quantity and quality
independently to generate explicit predictions of the species' responses
to climatic changes between Last Glacial Maximum (LGM) and present day.
We built ecological niche models and distribution models for 21 reptile,
mammal, and plant taxa from the Baja California peninsula inhabiting
lowland or highland environments. Geological data suggests the CCSM
global circulation model is a better representation of LGM climate for
the Baja California peninsula. Significant niche divergence was detected
for all clades within species, along with significant differences in the
niche breadth and area of distribution between northern and southern
clades. Most clades showed a reduction in distribution area towards LGM.
Further, niche marginality (used as a measure of habitat quality) was
higher during LGM for most clades, except for northern highland species.
Our results suggest that changes in habitat quantity and quality can
affect organismal response independently. This allows the prediction of
genomic signatures associated with changes in effective population size
and selection pressure that could be explicitly tested to support our
models.

\textbf{Keywords:}

Baja California peninsula, ecological niche modeling, effective
population size, Last Glacial Maximum, niche centroid, selection
pressure

\textbf{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; Rom\selectlanguage{ngerman}án-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 (\textasciitilde{}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.

\textbf{Materials and Methods}

\emph{Climatic data and characterization of the Baja California
Peninsula}

We characterized the current climatic conditions of the Baja California
peninsula by using 19 bioclimatic variables (Supporting Information)
with a spatial resolution of 1 km obtained from Worldclim (Fick \&
Hijmans, 2017). Additionally, we obtained data from two different global
circulation models (CGMs): the Interdisciplinary Research on Climate
(MIROC v3.2; Hasumi \& Emori, 2004) and the Community Climate System
Model (CCSM3; Collins et al., 2006), for characterizing the climate
during the Last Glacial Maximum (LGM; \textasciitilde{} 21 kya).

We calculated the difference between present-day and LGM conditions for
all temperature and precipitation variables for both GCMs. Since
previous work showed discrepancies between GCM conditions on the BCP
that affected SDMs (See Supporting Information for details), we compared
the GCM differences to paleoprecipitation proxy data published for
alluvial fan, pollen, lake core record, and midden data, across southern
California and the Baja peninsula to determine which GCM was more
consistent with paleoclimate data at the LGM in this region.

\emph{Species georeferenced records}

Our study focused on 21 taxa native to the BCP (Table 1), including
eight mammals, four plants and nine reptiles. We selected species for
which their genetic structure on the peninsula was previously published.
We aimed to represent species that inhabit different elevations
(highland or lowland), which we hypothesized could respond differently
to LGM conditions. We identified the number of genetic clades described
in previous studies for each taxon and classified them according to
their geographic location in southern (south of the Vizcaíno peninsula,
\textasciitilde{}27ºS), northern (north of \textasciitilde{}27ºS
including the Vizcaíno peninsula) and clades without north-south genetic
differentiation (unstructured). For each taxon we obtained georeferenced
records from the Global Biodiversity Information Facility
(\emph{https://www.GBIF.org}). Occurrences were manually filtered to
accurately represent each taxon distribution, and a minimum convex
polygon of each clade's distribution was used to assign occurrences
within a 10 km buffer to their corresponding genetic clade. The values
for the 19 bioclimatic variables (Table S1) were obtained from each
occurrence point.

\textbf{Table 1.} List of species selected for this study indicating
their corresponding taxonomic group (M: mammal; P: plant; R: reptile)
and elevation (H: highland; L: lowland). We also indicate the reference
(Ref) describing the species' genetic structure, along with the number
and location (N: north; S: south; -: unstructured) of described genetic
clades, and the type of genetic data (mit: mitochondrial; plastid;
nuclear; or RADseq) used to determine the genetic structure. Finally, we
show the number of occurrence records, the AUC value and the selected
variables to build the ecological niche model for each genetic clade.\selectlanguage{english}
\begin{longtable}[]{@{}lllllllllll@{}}
\toprule
\begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Species\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Tax\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Elv\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Ref\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Type of genetic data\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Genetic clade\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Loc\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
N\selectlanguage{ngerman}° Occ.\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
AUC\strut
\end{minipage} & \begin{minipage}[b]{0.07\columnwidth}\raggedright\strut
Variables\strut
\end{minipage}\tabularnewline
\midrule
\endhead
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Otospermophilus becheeyi}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
5734\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.924\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio3, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
121\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.984\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio9, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Sorex ornatus}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
-\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
476\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.926\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio7, bio14, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
4\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Spilogale gracilis}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
-\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
160\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.964\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio5, bio6, bio10\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
5\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Chaetodipus arenarius}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
4\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1887\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.935\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio6, bio8\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
6\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1569\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.986\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio5, bio11, bio12\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
7\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Chaetodipus spinatus}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
5\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3833\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.898\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio15, bio18\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
8\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
850\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.982\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio7, bio14, bio19\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
9\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Dipodomys merriami}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
6\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
61\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.971\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio8, bio9, bio11, bio18\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
10\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
40\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.991\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio3, bio11, bio13\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
11\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
43\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.969\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio4, bio7, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
12\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Neotoma bryantii}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
7\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
nuclear/mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
305\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.930\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio10, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
13\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
138\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.942\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio6, bio9, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
14\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Peromiscus maniculatus}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
M\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
8\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
-\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
5118\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.839\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio7, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
15\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Fouquieria columnaris}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
P\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
9\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
plastid\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
608\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.967\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio6, bio8, bio11, bio13\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
16\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
41\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.951\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio13, bio19\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
17\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Pinus cembroides} section\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
P\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
10\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
nuclear/ plastid\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1940\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.970\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio3, bio12, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
18\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
344\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.999\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio4, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
19\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Encelia farinosa}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
P\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
11\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
nuclear/ plastid\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
77\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.981\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio8, bio9, bio11\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
20\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
992\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.983\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio6, bio8, bio11, bio13\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
21\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Stenocereus gummosus}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
P\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
12\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
nuclear\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
-\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
860\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.958\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio5, bio12\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
22\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Crotaphytus vestigium}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
13\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
194\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.934\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio9, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
23\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
53\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.993\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio3, bio4, bio12, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
24\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
\emph{Elgaria multicarinata/velazquezi/} \emph{paucicarinata}\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
14\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
nuclear/mit\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
3441\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
0.970\strut
\end{minipage} & \begin{minipage}[t]{0.09\columnwidth}\raggedright\strut
Bio10, bio12, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
25\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
39\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.991\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio14, bio13, bio19\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
26\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
365\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.972\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio4, bio7, bio13\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
27\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Petrosaurus repens}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
15\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
RADseq\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
25\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.996\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio6, bio13\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
28\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
88\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.991\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio5, bio12, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
29\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
52\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.999\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio9, bio10, bio12\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
30\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Plestiodon skiltonianus/lagunensis}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
16\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1944\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.939\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio7, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
31\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
55\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.993\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio6, bio7, bio12\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
32\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Sceloporus orcutti}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
H\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
15\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
RADseq\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3785\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.886\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio5, bio12, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
33\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
613\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.988\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio8, bio9, bio15, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
34\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Callisaurus draconoides}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
15\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
RADseq\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2488\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.923\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio7, bio9, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
35\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
648\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.971\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio11, bio13, bio16, bio18\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
36\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
862\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.983\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio6, bio11\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
37\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
4\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
677\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.984\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio5, bio9, bio15, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
38\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
5\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1534\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio7, bio12, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
39\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Sceloporus zosteromus}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
15\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
RADseq\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
420\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.977\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio4, bio9, bio10\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
40\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
398\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.982\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio4, bio10, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
41\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Urosaurus nigricaudus}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
15\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
RADseq\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
725\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.951\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio3, bio15, bio18\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
42\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1337\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.931\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio5, bio8\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
43\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
65\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio1, bio2, bio11, bio12\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
44\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
4\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2149\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.993\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio3, bio4, bio15\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
45\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\emph{Uta stansburiana}\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
R\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
L\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
17\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
mit\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
N\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
10596\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.860\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio2, bio10, bio14\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
46\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
2\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
S\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
3269\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
0.976\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
Bio4, bio7, bio17\strut
\end{minipage}\tabularnewline
\begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage} & \begin{minipage}[t]{0.07\columnwidth}\raggedright\strut
1: Phuong et al. 2017; 2: Maldonado et al., 2001; 3: Ferguson et al.,
2017; 4: \selectlanguage{ngerman}Álvarez-Castañeda \& Ríos, 2011; 5: Álvarez-Castañeda \&
Murphy, 2014; 6: Álvarez-Castañeda et al., 2009; 7: Patton et al., 2007;
8: Kalkvik et al., 2012; 9: Martínez-Noguez et al., 2020; 10: Montes et
al., 2022; 11: Fehlberg \& Fehlberg, 2017; 12: Lozano, 2013; 13: McGuire
et al., 2007; 14: Leavitt et al., 2017; 15: Gottscho, 2015; 16: Richmond
\& Reeder, 2002; 17: Upton \& Murphy, 1997\strut
\end{minipage}\tabularnewline
\bottomrule
\end{longtable}\selectlanguage{ngerman}

\emph{Ecological niche models}

The ecological niche of each clade was modeled by estimating the niche
ellipsoid with the ``ntbox'' package (Osorio-Olvera et al., 2020a) in R
4.1.2 (R Core Team, 2021). Niche ellipsoids are a useful approximation
to the fundamental niche of a species and hence, allow for a functional
interpretation of the suitability values across clades (Osorio-Olvera et
al., 2019; Osorio-Olvera et al., 2020b). The niche ellipsoid represented
the 95\% confidence ellipsoid used by the clade in the multivariate
space built with bioclimatic data (Osorio-Olvera et al., 2020a). We used
the occurrence points from each genetic group, retaining 30\% of the
data as a testing set. We determined the best model to describe the
distribution of the genetic clades considering a subset of 3 or 4
variables from the bioclimatic variables after randomly removing one of
each pair with a correlation higher than 0.95. The best model was
selected based on the area under the receiver operating characteristic
curve (AUC).

\emph{Niche differentiation between clades}

To assess climatic niche differentiation between clades, we calculated
the niche overlap based on niche ellipsoids with the ``ellipsenm''
package (Cobos et al., 2020) in R. The niche overlap corresponds to a
value between 0 and 1, where 1 represents complete overlap and 0
represents no overlap. Niche overlap was calculated with the first three
principal components obtained from a principal component analysis (PCA)
of all scaled bioclimatic variables (See Supporting Information for
details). We compared all clade pairs within taxa, and significance was
obtained from 1,000 bootstrap replicates.

\emph{Niche breadth}

Niche breadth was calculated for each clade in the multivariate space
built from the PCA of all bioclimatic variables of current climatic
conditions. For this, the area of the minimum convex polygon from
occurrence points for each genetic clade within the first two dimensions
of the multivariate climatic space (67.05\% of variance) was calculated
with the ``adehabitatHR'' (Calenge, 2023) and ``sp'' (Pevesma \& Bivand,
2005) packages in R. Significant difference of niche breadth was tested
among clade location within taxa (north, south, or unstructured),
taxonomic group (mammal, plant, or reptile) and between elevation
(highland or lowland), using a generalized linear mixed model (GLMM) in
R with the ``lme4'' package (Bates et al., 2015) with a ``gamma''
distribution and an ``inverse'' link function, and including each taxon
as a random variable.

\emph{Projection to present-day and LGM climates}

The niche ellipsoid of each genetic clade, corresponding to the model
with the highest AUC value, was projected onto the present-day geography
to obtain each clade's predicted distribution. Distribution models were
binarized between suitable and non-suitable conditions by using a 10\%
of omission criterion. Then, we projected the niche ellipsoid to LGM
climate using MIROC and CCSM GCMs. The amount of geographic area
corresponding to suitable conditions for each clade was calculated for
present-day and LGM climate in R with the ``landscapemetrics'' package
(Hesselbarth et al., 2019). Further, we calculated the proportional
change in area for each clade by dividing the LGM-predicted area by the
present-day predicted area. Significant differences in the proportional
change in area were tested among clade location (north, south, or
unstructured), taxonomic groups (mammal, plant, or reptile), and
elevation (highland or lowland), using a single GLMM in R with ``lme4''
using a ``gamma'' distribution and ``inverse'' link function, including
each taxon as a random variable.

\emph{Niche marginality}

As a measure of habitat quality, we used two approaches for assessing
niche marginality for each genetic clade as well as changes in niche
marginality from LGM to present. First, we calculated the present-day
marginality as the Mahalanobis distance between the centroid of the
niche ellipsoid from each clade to the centroid of the available
multivariate space in the PCA of current climatic conditions with the
``philentropy'' package (Drost, 2018) in R. We also calculated the LGM
marginality as the Mahalanobis distance between the clade's niche
centroid and the centroid of LGM available conditions in this same
multivariate space. We then compared the niche marginality (i.e.
Mahalonobis distances) between LGM and present by constructing a GLMM
that included time period (LGM vs present), clade location (north,
south, or unstructured), taxonomic group (mammal, plant, or reptile) and
elevation (highland or lowland) as factors, including taxon as a random
variable, and using a ``gamma'' distribution and ``inverse'' link
function.

For the second measurement of marginality, for each genetic clade we
obtained the suitability values for each cell from the raster
projections of the niche models onto geographic space with the
``raster'' package (Hijmans, 2023) in R. We retained only values from
cells with suitability above the 10\% omission rate threshold. Then,
each value was converted to niche marginality between 0 and 1, defined
as the inverse of suitability with the formula:

\emph{1 - ((s -- min(s)) / (max(s)- min(s)))}

Where ``\emph{s} '' corresponds to the suitability values obtained from
the raster projections, and ``\emph{min(s)} '' and ``\emph{max(s)} ''
correspond to the minimum and maximum suitability values from the model,
respectively. Then, we calculated the kernel density distribution of
marginality within the suitable conditions with the ``density'' function
in R, which represents the relative amount of area of different
marginality values within suitable conditions. The calculation of the
density distribution of marginality was done for the present-day and LGM
distribution models. Then, we calculated the change in the marginality
distribution between LGM and present by subtracting the kernel density
curves from both time periods. Finally, to identify clusters of taxa
that showed similar changes in their marginality density distribution
between LGM and present, the density curves were hierarchically
clustered with the ``dad'' package (Boumaza et al. 2021) in R by
calculating the Hellinger's distance between density curve pairs.

\textbf{Results}

\emph{Past climatic conditions on the Baja California peninsula and
choice of GCM}

We consulted geological literature to determine which GCM was best
supported by paleoprecipitation proxies, which included alluvial fan,
pollen, lake core record, and midden data across southern California and
the BCP (Supporting Information). Unlike global climate, literature
indicates that the BCP was generally wetter than present at the LGM
(Lora, 2018; Lyle et al., 2012), culminating with an El Niño-like
wettest period during the Late Pleistocene-Holocene transition
\textasciitilde{}14.5-10 ka (Antinao \& McDonald, 2013). This was driven
by strengthening East Pacific (westerly) precipitation that affected
mainly southern California and the northern BCP in the form of winter
rain and less seasonality (Antinao \& McDonald, 2013; Antinao et al.,
2016). On the other hand, while the south would have been drier overall
after LGM, there is evidence from alluvial fan deposits and offshore
cores that despite less precipitation, the precipitation came as
stronger, and possibly more frequent, tropical cyclones reaching the
southern BCP (Antinao et al., 2016). The Pacific High weakened
\textasciitilde{}17-11 kya and allowed warm tropical waters to move
northward, partially strengthening the North American Monsoon (NAM) and
leading to increasingly wetter conditions in the south comparable to
what is observed today (Antinao et al., 2016). After that, the southerly
NAM was stable but weaker, contributing less precipitation at least in
part due to cooler Gulf of California sea surface temperatures 11--8 ka
and a limited northward progression of those storms due to presence of
the Pacific High.

Considering total annual precipitation (bio12), CCSM shows drying in the
southern peninsula and increased wetness in the north (Figure 1b), which
is in agreement with the paleoprecipitation data, whereas MIROC shows
substantially wetter conditions throughout the peninsula (Supporting
Information). Furthermore, the precipitation of the wettest month
(bio13) shows a drying in the CCSM models in the south and slightly
increased precipitation in the north, but the MIROC model shows wetter
conditions throughout (also evident in bio18). CCSM shows a slight
strengthening of seasonality (bio15), while MIROC shows patchy decrease
of moderate magnitude, the latter of which is more in line with the
paleoprecipitation proxy data. Despite this last observation, we chose
the CCSM GCM as the overall best model for our analyses because it
appears to be more consistent with paleoprecipitation data particularly
as it relates to the increased precipitation in the north and decreased
effect of NAM precipitation and tropical storms in the south.\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/image1/image1}

\end{center}
\end{figure}

\textbf{Figure 1.} Change in climatic conditions on the Baja California
peninsula between LGM and present day, considering the CCSM GCM. Circles
represent georeferenced sites from the literature of paleoprecipiation
proxy data that were used to evaluate regional accuracy of CCSM vs MIROC
GCMs (Supporting Information).

\emph{Ecological niche models}

We modeled the ecological niche of 47 clades from 21 taxa (Table 1).
After filtering, our final dataset included a total of 65,373
georeferenced records representative of the known distribution of the
studied species (range per clade 25-10,596). One out of
four\emph{Dipodomys merriami} clades presented only 7 occurrence
records, therefore this clade was not included in further analyses. AUC
values for the niche models were on average 0.961 (median: 0.972; range
0.839-0.999; Supporting Information includes other model evaluation
metrics). The three most common variables selected to build the models
were mean annual temperature (bio1), temperature seasonality (bio4) and
precipitation seasonality (bio15, Table 1).

\emph{Between clades niche divergence}

We used the first three dimensions of a PCA of current climatic
conditions (84.97\% of variance; see Supporting Information for details)
to calculate niche overlap between populations. Between-clade climatic
niche divergence was detected as overlap values were significantly lower
than expected by chance for all clade pairs within species (Figure 2a).
Overlap values ranged from 0.000 to 0.302 (Supporting Information). In
general, northern clades were located towards positive values of PC1 and
PC2 (i.e. inhabit cooler environments with higher winter precipitation),
whereas southern clades were mostly on negative values of PC1 and PC2
(i.e. warmer environments with higher summer precipitation). Significant
differences were detected for the niche breadth between southern,
northern and unstructured clades (Supporting Information). In general,
northern and unstructured clades presented wider niches than southern
clades (Figure 2b).\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/image2/image2}

\end{center}
\end{figure}

\textbf{Figure 2.} Ecological niche and distribution
analyses.\textbf{A.} Niche overlap between northern and southern clades
for\emph{Sceloporus zosteromus} . \textbf{B.} Niche breadth for all
genetic clades. \textbf{C.} Present day distribution area for all
clades.\textbf{D.} Change in distribution area from LGM to present for
all clades. \textbf{E.} Example of distribution model for \emph{S.
zosteromus} for present day and LGM CCSM climatic conditions, shows a
contraction of the distribution for the northern and southern clades.
The gray outline indicates the sea-level boundary for LGM conditions.

\emph{Contraction of the distribution area to LGM for most clades}

When we projected the ecological niche onto geographic space (Figure 2e)
and quantified the area occupied by each clade we detected a significant
effect of clade location on the present-day area (Supporting
Information), where northern and unstructured clades distribute over
larger areas (Figure 2c) than southern clades. When projecting the
models to LGM -- CCSM conditions (Figure 2e), we detected that several
clades showed a reduction in their geographic area (Figure 2d;
Supporting Information shows projections to LGM using the MIROC GCM).
The species \emph{F. columnaris} did not present suitable area during
LGM conditions for the CCSM GCM. No significant effect of clade was
detected on the proportional change in area (Supporting Information).
Most unstructured clades showed an increase in their distribution area
during LGM (Figure 2d).

\emph{Increased niche marginality during LGM for most taxa except for
highland northern clades}

When assessing the change in centroid-based niche marginality between
LGM and present, a significant effect was detected for the interaction
between time and clade location (Supporting Information). In general, a
decrease in marginality towards present day was detected for most
highland and lowland clades (Figure 3), and three highland southern
clade outliers (\emph{Pinus cembroides} , \emph{Elgariapauciarinata} and
\emph{Plestiodon} \emph{lagunensis} ) showed a strong decrease
(Supporting Information). Five highland northern and two lowland
southern clades showed an increase in centroid niche marginality to
present day (black labels, Figure 3).\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/image3/image3}

\end{center}
\end{figure}

\textbf{Figure 3.} Centroid niche marginality at LGM and present for
each genetic clade for highland \textbf{(A)} and lowland
\textbf{(B)}taxa. A decrease in niche marginality is observed for most
clades, except for five highland northern clades and two lowland
southern that show an increase in marginality for present day climate,
indicated with their numeric identifier according to Table 1. Figure not
showing 3 highland outliers (see Supporting Information for graphs with
the outliers).

As a second measure of niche marginality, we evaluated the change in the
proportion of different marginality values within the suitable area for
each clade for present day climate and LGM, and clustered the different
clades based on the similarity of their change in normalized area of
different marginality values (Figure 4a). The species \emph{F.
columnaris} was not included in this analysis since it did not present
suitable areas for LGM GCM climatic conditions. The best supported
number of clusters was five (Figure 4b) that can be qualitatively
described as taxa with: i) much more marginal area at LGM, ii) much more
marginal area at present, iii) slightly more marginal area at LGM, iv)
slightly more marginal area at present, and v) similar marginality at
present and LGM. Most highland species clustered in the more marginal
area at present (group ii; Figure 4). There was no clear grouping by
taxonomic group (plant, mammal or reptile) or location of the genetic
clade.\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/image4/image4}

\end{center}
\end{figure}

\textbf{Figure 4.} Change in the proportion of marginal conditions
within suitable area for each clade. \textbf{A.} Cluster analysis
showing five groups according to their changes in the normalized
marginality area between LGM and present (i: More marginal area at LGM,
ii: more marginal area at present, iii: slightly more marginal area at
LGM, iv; slightly more marginal area at present, and v: similar
marginality at present and LGM). Highland taxa are highlighted in green.
Pink (N) and blue (S) indicate location of genetic clade; ``-``
indicates unstructured clades. In the heatmap, red represents more area
of a determined marginality value at LGM. \textbf{B.} Normalized area
distribution of each marginality values for LGM CCSM and present-day
climate for some example clades from each cluster.

\textbf{Discussion}

Environmental changes can affect the distribution, abundance, and allele
frequency distributions of natural populations (Foden et al., 2019;
Rom\selectlanguage{ngerman}án-Palacios \& Wiens, 2020; Aguirre-Liguori et al., 2021) by
modulating the quantity and quality of available habitats. Organismal
response will depend on intrinsic characteristics, which determine
whether species persist in a location, shift their distribution and
track suitable conditions, or evolve to expand their niches. In this
study, we assessed how different taxa on a climatically heterogeneous
landscape, the Baja California peninsula, have responded to
environmental changes between LGM and present day with the aim of
generating predictions about the effects of past climatic changes on
population abundance and selection pressure.

\emph{The CCSM GCM better described LGM climate on the Baja California
peninsula}

Previous SDM studies on the Baja California peninsula have shown
differences in their results based on the GCM used (Guevara et al.,
2019). Using a GCM that adequately represents the climatic patterns in
the study area is crucial for generating accurate niche models. Overall,
we chose CCSM for hindcasting our SDMs because it shows higher
consistency with multiproxy paleoprecipitation data provided by
different sources (Antinao \& McDonald, 2013; Antinao et al., 2016),
particularly related to the increased precipitation in the north and
decreased effect of NAM precipitation in the south. Both models (CCSM
and MIROC) could not consistently capture the decrease in seasonality,
though MIROC performed slightly better, and indicates that for species
with strong circannual rhythms MIROC may be the better model. The
northern peninsula may have been wetter at the LGM than CCSM predicts,
suggesting that hindcasted SDMs for northern clades may slightly
misrepresent habitat availability. In general, in a region that lies at
the interface of several weather/climate systems whose components change
in both interrelated and independent ways based on oceanic, land, and
atmospheric features, it might be expected that GCMs perform differently
here while they perform well globally. It is possible that the very
narrow aspect of the peninsula, its high topography that traps some
moisture sources (i.e. fog), and the stark oceanographic differences
between the Pacific Ocean and Gulf of California on either side make
paleoclimate predictions in this region challenging. On the other hand,
the same diversity and complexity of microclimates seem to have played a
role in the diversification of niches and accumulation of genetic
divergence within species.

\emph{Niche patterns on the Baja Peninsula}

Genetically divergent groups on the peninsula presented ecological niche
divergence for all between-clade comparisons (Supporting Information).
This agrees with previous studies including some of the same taxa
(Cab-Sulub \& Álvarez-Castañeda, 2021), and expands the niche divergence
pattern further than just North-South of the Vizcaino region, but also
between clades within a same region of the peninsula. This suggests that
some species could have adapted to the high diversity of available
environmental conditions, and could explain the high variation in the
location of genetic breaks previously documented (Dolby et al., 2015;
Araya-Donoso et al., 2022).

Niche breadth differed between clades located in the north and south of
the peninsula (Figure 2), whereas elevation and taxonomic group showed
no effect on niche breadth. The niche breadth was wider in northern
clades than in southern clades, which could shape how populations
responded to glacial oscillations (Carscadden et al., 2020). This is
associated with a generally wider heterogeneity of available climatic
conditions in the north than in the south. However, after standardizing
by geographic area, the niche breadth in the north and south are similar
(Supporting Information). It is important to note however that the niche
utilization at the scale of the organism can differ greatly from
predictions on a macroenvironmental scale (Ficetola et al., 2018).
Therefore, there may be less niche divergence than predicted by these
models if organisms are experiencing microclimates that are less
apparent at a macro scale.

\emph{Decreased habitat area for most taxa}

We projected each clade distribution onto geographic space for present
day and LGM climate. Consistent with the niche breadth results, northern
clades distributed over wider areas for present day climate than
southern clades (Figure 2). Most clades showed a reduction in their
distribution area towards the eastern coast of the southern half of the
peninsula (BCS) when projecting our models to LGM (Supporting
Information). During LGM the peninsula was colder, drier in the south
and wetter in the north (Figure 1, Antinao \& McDonald, 2013; Antinao et
al., 2016), conditions that could have been more challenging for
desert-adapted species and therefore constrained their distributions. In
general, organisms inhabiting arid sub-tropical regions have been
described to show heterogeneous responses to Pleistocene climatic
variation compared to organisms from temperate regions, since their
response is highly dependent on local precipitation patterns (e.g.
Anadón et al., 2015). The population contraction and subsequent
isolation during Pleistocene glaciations could have produced and/or
strengthened the divergence between genetic groups (Dolby et al., 2015;
Araya-Donoso et al., 2022; Dolby et al., 2022).

Previous distribution modeling studies in this area have detected
different patterns of LGM distribution. Some studies have detected
population expansion towards LGM (Graham et al. 2014; González-Trujillo
et al. 2016; Harrington et al. 2017; Arteaga et al. 2020), whereas
others have detected range reductions (Valdivia-Carrillo et al. 2017;
Klimova et al. 2017). Moreover, Cab-Sulub \& Álvarez-Castañeda (2021)
detected different patterns depending on the genetic clade within each
taxon, in which southern clades showed area reduction and northern
clades showed expansion. The differences between those studies and ours
could be due to the modeling algorithm since all those studies
implemented Maxent and we used minimum volume ellipsoids (See Supporting
Information for further discussion).

\emph{Different patterns of niche marginality during LGM for highland
and lowland species}

We incorporated two measures of niche marginality in our analyses to
assess habitat quality within our models, which allowed us to infer
changes in population fitness and putative selection pressure from LGM
to present. We detected higher centroid niche marginality during LGM for
most clades, particularly southern highland clades (Figure 3a).
Moreover, within suitable areas some clades presented a higher
proportion of more marginal conditions during LGM (Figure 4). Both
approaches showed consistent results, however the full distribution of
marginal areas provided a more detailed description of how habitat
quality changed through time. Despite a general reduction in the amount
of habitat for all clades and species during LGM, changes in habitat
quality between LGM and present day differed among desert-adapted
lowland taxa and cold-adapted highland taxa. For lowland desert-adapted
species, available environmental conditions were in general more
challenging during LGM (Figure 3, Figure 4), and in the desert regions
from the southern peninsula habitat quality improved more LGM to present
relative to the north (Figure 3, Figure 4). In contrast, for most
highland species habitat quality seems to have declined since LGM, but
particularly in the Northern part of the Peninsula (Figure 3, Figure 4).
Highland species generally present adaptations to cold environments,
such as sustained activity during suboptimal temperatures in the
lizard\emph{Elgaria multicarinata} (Kingsbury, 1994) or the structure of
needles in \emph{Pinus} species (Jankowski et al. 2019). Highland
species being favored during LGM conditions is consistent with studies
from other regions such as the Afromontane forests range expansions in
the Horn of Africa (Casas-Gallego et al., 2023), or
\emph{Polyepsis}woodlands on the Andes Mountains (Zutta \& Rundel,
2017).

\emph{Model predictions that can be tested with genetic data}

Integrating ENMs and SDMs with genomic data can be used to test whether
our inferences about species responses to climate change are accurate
and relevant and hence, make better predictions of potential responses
to future climate change. The independent assessment of habitat quality
in ecological niche models constitutes an improvement since, in addition
to the inferences about changes in the species' distribution ranges, by
analyzing changes in niche marginality between LGM and present day we
can infer changes in population fitness and selection pressure within a
species' distribution (Figure 5a).

An example is the northern clade of \emph{Plestiodon}
(i.e.\emph{Plestiodon skiltonianus} , highland species) which shows a
contraction of its distribution from LGM to present (Figure 5b, Figure
5c), in addition to a decrease in habitat quality (i.e. increased
marginality) at its northernmost distribution. Populations of this
species at these locations should show signatures of a bottleneck along
with increased selection pressure associated with higher temperatures
and lower precipitation in present day climate (Figure 1, Figure 5d).
This could be evidenced by adaptations in thermoregulation or water
physiology, and positive selection should be focused to genes associated
with these processes such as aquaporins (e.g. Araya-Donoso et al., 2021)
or heat shock proteins (Chen et al., 2018). An example of a lowland
desert adapted taxon is the southern clade of the packrat \emph{Neotoma
bryanti} (Figure 5e), which exhibits a geographical expansion towards
the north from LGM to present (Figure 5f), associated with increased
habitat quality (i.e. decreased marginality) in the central populations
(Figure 5g). Stable populations between LGM and present for this species
should reflect an increase in effective population size, and could show
signatures of natural selection associated with LGM climate (Figure 5f,
Figure 5g) while the northern part of the range may be expected to have
lower diversity as a consequence of range expansion as well as surfing
of deleterious alleles (Escoffier et al., 2008; Gilbert et al., 2018).

These predictions can be tested with genomic data, evaluating if the
patterns of genetic variation reflect the expected changes in effective
population size and signatures of selection predicted by our models.
According to published genetic data, the mammals \emph{Chaetodipus
spinatus} (Álvarez-Castañeda \& Murphy, 2014), \emph{Spilogale
gracilis}(Ferguson et al., 2017), and \emph{Otospermophilus becheeyi}
(Phuong et al., 2017) show population size reduction during LGM, which
is in agreement with our prediction of reduced suitable area or
increased marginality in the LGM distribution models (except for
\emph{C. spinatus} ). Whole genome sequencing data from populations
across the peninsula would be required to evaluate the selection
pressure predictions from this study. An example of this approach is
Farleigh et al. (2021), who used genomic data to infer changes in
population size and potential genes under selection for the lizard
\emph{Phrynosoma platyrhinos} across the North American deserts,
formally testing previous hypotheses about demographic changes and
adaptation to different climates (Jezkova et al., 2016).\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/image5/image5}

\end{center}
\end{figure}

\textbf{Figure 5. A.} Diagram representing that ENMs and SDMs can be
applied to infer changes in Ne and selection pressure for natural
populations. \textbf{B-D.} Inference of population
contraction\textbf{(D)} and increased marginality \textbf{(E)} areas
between LGM and present within the distribution for the northern clade
of\emph{Plestiodon} . \textbf{E-G.} Inference of areas with population
expansion \textbf{(F)} and decreased marginality \textbf{(G)} for the
southern clade of \emph{Neotoma bryantii} between LGM and present.

\textbf{Conclusions}

Assessing changes in quantity and quality of available habitats allows
the generation of more detailed interpretations of population dynamics
in response to past climate changes, and predictions of future changes
in climatic conditions. SDMs are useful to infer changes in distribution
of organisms, and here we show how niche marginality can be used as a
proxy to predict species' abundance and selection pressure. Results
showed that species on the Baja California peninsula responded to
changes in climatic conditions based on their ecological niche
characteristics. Some highland clades were favored during LGM climatic
conditions, since besides a decrease in the area of suitable conditions
they may have presented increased fitness within those available
habitats due to those habitats having lower niche marginality. This
demonstrates the decoupling between habitat quality and quantity
relevant to the evolution of populations. On the other hand, lowland
desert clades seem to have better habitat conditions under present
climates in terms of habitat quantity and quality. Overall, we were able
to generate explicit predictions about population history that can be
tested with genomic data to generate a better understanding of
population dynamics driven by climatic changes in habitat quantity and
quality.

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