Introduction
Due to their isolation and high degree of endemism, South American
temperate forests are considered of great ecological and evolutionary
importance (Smith-Ramirez et al., 2007). In Chile, temperate forests
stretch from the 35°S down to the 55°S, forming a continuous area that
can be considered a “biogeographic island” separated by impassable
barriers (deserts, mountains, and oceans) from the rest of the ancestral
sources of its biota (Villagrán 1991). As a result, the climate and
topography characterizing the narrow strip (2000 km long and 120 km
wide) of Chilean temperate forests generate high heterogeneity of forest
and soil types, climatic conditions, and disturbance regimes (Loguercio
et al., 2018). Adaptive processes linked to persistence in a mosaic of
heterogeneous habitats may have contributed to plant species
diversification in the temperate forests of southern South America
(Johnson et al., 2014; Prunier et al., 2017). In the same way, within
species genetic divergence of plants with extensive distribution under
strong natural environmental gradients could also reflect the action of
selection (Saldaña et al., 2007, Zeppel et al., 2014; Grossiord et al.,
2004). The effect of contrasting climatic and edaphic features on
phenotypic and genetic diversity has been observed in various temperate
plants (Saldaña et al., 2007; Torres-Díaz et al., 2007). For instance,
the existence of distinct ecotypes has been linked to contrasting access
to water and snow winter coverage in Embothrium coccineum J.R.
Forts. & G. Forst (Dimitri, 1972), a widespread tree that inhabits the
temperate forest of South America (Zegers 1994). This species is an
endemic tree of Gondwanan origin with a distribution range matching the
extent of the temperate forest biome in Chile and Argentina, which
exhibits different phenotypes throughout its distribution (Alberdi y
Donoso, 2004; Chalcoff et al., 2008). The distribution of these ecotypes
is concordant with the pattern of genetic structure observed using
isoenzymatic genetic markers (Souto and Premoli, 2007), suggesting thatE. coccineum populations across the species range may be locally
adapted to distinct environmental conditions (Souto and Premoli, 2007).
Besides the possible effect of current selective regimes, climate shifts
during the Pleistocene have also strongly altered the spatial patterns
of genetic variation of many southern South American taxa (Vidal-Russell
et al., 2011; Turchetto-Zolet et al., 2013). During the Last Glacial
Maximum (LGM, 25.000 years Before Present, BP), due to the presence of
ice caps, a large expanse of temperate forest located between the 42 °S
and the 56 °S disappeared (Rabassa et al., 2005). Glacial maxima
triggered a rapid range shift, with most temperate South American
species surviving only in glacial refugia located north of the 42°S
(Allnutt et al., 1999; Premoli et al., 2000, Sérsic et al., 2011). Some
cold tolerant species, as E. coccineum, were also able to survive
in refugia embedded within the main glaciated area in localities where
microclimate, topography or geothermic activity hindered the formation
of the ice cap (Allnutt et al., 1999; Premoli et al., 2000, Sérsic et
al., 2011). These areas could represent sources of regional diversity
recovery after deglaciation (Comps et al., 2001). The presence of 11.000
years BP cold tolerant plants pollen fossil in areas covered by ice
during the LGM (Fesq-Martin et al., 2004, Steubing et al., 1983) and
results of genetic studies based on sequences of chloroplast genes or
genotyping of nuclear isoenzymatic markers (Vidal-Russel et al., 2011;
Souto and Premoli, 2007) suggest a complex glacial-interglacial history
in this species.
Recent developments in high throughput sequencing technologies and
population genomics have allowed to distinguish the influence of past
environmental changes and selection to the current environmental
conditions on the spatial patterns of genetic variation in both South
American plants and animals (Turchetto-Zolet et al., 2013; Hasbún et
al., 2016; Varas-Myrik et al., 2021). If divergent natural selection has
led to genetic differentiation between populations of E.
coccineum along environmental gradients characterizing South American
temperate forests, a pattern of isolation by the environment (IBE; Wang
and Bradburd, 2014) should be expected. Indeed, when selection against
immigrant limits gene flow among distinct environments, genetic
differentiation increases with environmental differences (Wang and
Summer, 2010; Wang and Bradburd, 2014). To test for the existence of
IBE, the level of correlation between genetic differentiation and
environmental distances should be contrasted against the one observed
between genetic differentiation and geographic distances (isolation by
distance; IBD; Slatkin, 1993). IBD could be considered as a null model
for which genetic differentiation increases with geographical distance,
given the local accumulation of genetic differences when the dispersion
between populations is geographically restricted. In E.
coccineum , gene flow could be limited by constraints on pollen
transport that is linked to the distribution and behavior of pollinators
(i.e., more than 20 species including birds and insects are reported as
pollinators of E. coccineum ; Chalcoff et al., 2008) and
anemochorous seed dispersal (Rovere and Premoli, 2005).
The
main goal of this study was to evaluate the effects of historical and
contemporary landscape features affecting the genetic diversity and
connectivity of E. coccineum throughout its natural distribution
using SNPs obtained by genotyping-by-sequencing (GBS). Patterns of
genetic structure were evaluated independently using SNPs found in
genomic regions that may be subject to selection (i.e., outlier loci)
and all loci. We hypothesized that patterns of genetic variation inE. coccineum will reflect both the impact of historical processes
(i.e., glacial / interglacial cycles during the Pleistocene) and
contemporary landscape features including the selective effect of
environmental heterogeneity.