Paleoclimatic distribution simulations
Ecological niche modeling (ENM) was used to test the influence of
paleoclimate on the distribution of A. mantiqueira and A.
alalia . The occurrence points from each species were obtained from an
extensive dataset (Gueratto et al. submitted ) and mapped in a
grid cell with 5 arc-minutes (~10km). As result, a total
of 21 occurrence points were recorded for A. alalia , and 78 forA. mantiqueira . The number of occurrences of the species at each
gridded cell was standardized to avoid oversampling of specific
environmental conditions (abundance biases).
In order to understand the pattern of spatial expansion and retraction
of both Actinote species over glacial cycles, the models were
created from the present to 800 thousand years ago (kya), a period that
covered nineteen glacial-interglacial cycles. The climate variables of
the Last Glacial Maximum (21 kya), Last Interglacial Maximum (LIG – 130
kya) and Upper Pleistocene (~787 kya) periods were
obtained from the Paleoclim database
(http://www.paleoclim.org/)
(Fordham et al. 2017, Brown et al. 2018). To avoid collinearity between
the climate variables, five axes were selected through Principal
Component Analysis (PCA), accounting for the greatest variation in
temperature and precipitation from the current climate data in the
Neotropical region. The coefficients of the PCA were then applied to
find the axes’ scores from the past climates with the purpose of
maintaining the dimensionality among the climate predictors (see the
protocols in Manly et al. 1994, Legendre & Legendre 1998, Amaral et
al., 2021). The climate conditions (PCA axes) were interpolated by using
the global stacked δ18 Oxygen curve (Lisiecki & Raymo 2005) as a
covariate (see Lawing & Poly 2011, Raposo et al. 2021). Interpolation
was calculated each one thousand years between present time and 600 kya;
and each two thousand years in the interval from 602 to 786 kya.
As each algorithm present distinct prediction according to the different
niche breadth of the specie (Qiao et al. 2015), their combined use may
increase the accuracy of predictions by considering different niche
tolerances in the potential distribution of species (Araujo & New 2007,
Diniz-Filho et al. 2009). Therefore, five different mathematical
algorithms were used: Bioclim (Nix 1986), distance method Domain (Gower
distance; Carpenter et al. 1993), support vector machines (SVM; Tax &
Duim 2004), maximum entropy – Maxent (Phillips & Dudík 2008) and
Ecological-Niche Factor Analysis (ENFA; Hirzel et al. 2002). As a way of
evaluating the generated models, the occurrence points were randomized
in two groups, training and testing, which contain 70% and 30% of the
occurrence points, respectively. The model’s performance was evaluated
with the D statistic, which considers only presence records and weights
the true positive rate (TPR) by the inverse of the proportional
predicted distribution area (pi): D = TPR∗(1-pi) (Pearson et al. 2007).
Threshold values using maximum sensitivity and specificity were
calculated in order to maximize the correctness of presences and
absences. After defining the thresholds, a prediction map of each
species was obtained following the ensemble technique (Araujo & New
2007).
All modeling methods describe above were followed separately to build a
climate-based to each geological period, thus resulting in 695 final
consensus maps for each of the two Actinote species: models at
each one ky BP (between present and 600 ky BP) and 2 ky BP (between 602
and 786 ky BP) intervals. The glacial and Interglacial periods were
delimited according to Marine Isotope Stages (MIS) proposed by Lisieck
& Ramos (2005). All analyzes were performed in R 4.0.2 (R Development
Core Team 2010).
Results
Genotyping-by-Sequencing
Statistics
The number of reads for each run per lane ranged from 348 to 352
million. Sequencing quality across all bases was above 32 Phred Score,
no adapters were found in the sequences, and the missing (N) content in
all bases was not significant. After the demultiplexing, 96.7% of reads
were retained, and 266,933 loci were genotyped with a mean coverage of
89.9X and a standard deviation of 35.8X.