1 | Introduction
Introgression is the transfer of alleles from one taxon (donor) into
genomes of another taxon (recipient) through hybridization,
recombination, and backcrossing (Anderson 1953; Barton and Hewitt 1985).
Generally, alleles introgressed from the donor taxon can be deleterious,
because of conflicting interactions in the genomes and unfavorable
phenotypes in the environment of the recipient taxon (Burke and Arnold
2001; Goulet et al. 2017). Thus, introgressed alleles will be purged
from the recipient genomes, and the genetic integrity of each taxon can
be maintained (Rieseberg and Carney 1998). However, in specific
environment, where the donor-like phenotypes are more adaptive than the
recipient phenotypes, introgressed alleles can be selected and fixed in
the recipient genomes (Anderson and Stebbins 1954; Suarez-Gonzalez et
al. 2018c). Such environment-dependent adaptive introgression has been
found in some plants, resulting in the expansion to novel habitats and
the creation of different ecotypes in the recipient taxa (Martin et al.
2006; Rieseberg et al. 2007; Whitney et al. 2010; Arnold et al. 2016).
Adaptive introgression tends to occur at distributional range margins of
either taxon, where hybridization with the other taxon is frequent due
to reduced opportunity of mating within marginal populations, and
introgressed populations of the recipient taxa can colonize habitats
suitable for the donor taxa (Chhatre et al. 2018; Ma et al. 2019; Menon
et al. 2021; Rendón-Anaya et al. 2021). This process is thought to
contribute colonization and range shift of forest trees during past
climate change and offer an option of forest management under future
climate change (Petit et al. 2004; Hamilton and Miller 2016).
Oaks (genus Quercus , Fagaceae) are temperate forest trees in the
northern hemisphere and are often interfertile among species (Denk et
al. 2017). Introgression between oak taxa has long been proposed
(Stebbins et al. 1947; Sork et al. 2016), and their genomes are regarded
as phylogenetic mosaics of different origins (Kim et al. 2018; Hipp et
al. 2020). Oaks inhabiting heterogeneous environments usually have
different phenotypic and genetic variations (Ortego et al. 2014; Riordan
et al. 2016; Cavender-Bares 2019) and often exhibit local adaptation to
indigenous environments (Sork 2018; Leroy et al. 2020). In northern
Japan, there are two species of white oaks (section Quercus ),Q. mongolica Fischer ex Ledebour var. crispula (Blume) H.
Ohashi (Qc ) is common in inland habitats, and Q. dentataThunberg ex Murray (Qd ) occurs in coastal habitats (Matsumoto et
al. 2009). In northern Hokkaido, Qd trees are rare because this
area is the northern distributional limit of Qd , whereasQc trees are abundant because Qc is distributed to more
northern area, Sakhalin. In the northernmost area of Hokkaido, a coastalQc ecotype with unique traits, which are similar to Qdphenotypes and tolerant to coastal stress, occurs in coastal forests
(Nagamitsu et al. 2019). Some taxonomists regarded this coastalQc ecotype as a hybrid taxon Q. × angustilepidotaNakai (Qa ) between Qc and Qd (Ohba 2006; Aizawa et
al. 2021). Multi-locus nuclear microsatellite genotypes supported this
hybrid origin (Nagamitsu et al. 2019), and genome-wide single nucleotide
polymorphism (SNP) genotypes demonstrated environment-dependent
introgression from Qd to Qc , resulting in Qa that
included hybrids after the first generation of backcross to Qc(Nagamitsu et al. 2020). Thus, introgression of Qd alleles toQc genomes at loci associated with traits adaptive to coastal
environment is expected but has not been confirmed yet.
Oak trees in coastal habitats suffer from various stress, such as wind,
salinity, drought, heat, substrate instability, and nutrient scarcity
(Hesp 1991). For example, strong wind and salt spray in winter cause the
mortality of buds in the upper parts of shoots, resulting in frequent
dieback of shoots, slow elongation of stems, and low canopy height of
coastal oak forests (Asai et al. 1986). These stresses are likely to
cause natural selection in leaf and shoot traits, leading to local
adaptation (Ramírez-Valiente et al. 2010; Ciccarelli and Bona 2022).
Common-garden experiment using inland and coastal test sites is
effective to show local adaptation in Qc and Qd .
Relatively higher performance of Qa trees with Qd -like
phenotypes of leaf and shoot traits in coastal sites than in inland
sites will indicate the adaptation of these traits to coastal habitats.
Difference in phenotypes among admixed trees between inland and coastal
habitats depends not only on genetic and environmental variations but
also on their interaction, namely phenotypic plasticity
(Ramírez-Valiente et al. 2010). Common-garden experiment is useful to
elucidate phenotypic plasticity and to discriminate genetic variation
from environmental variation in phenotypes.
Phenotypes of admixed recombinants in common gardens enable us to detect
loci associated with focal traits (Rieseberg and Buerkle 2002). This
approach is referred to as admixture mapping and is useful in long-lived
and large-sized organisms, for which pedigrees from artificial crosses
are difficult to obtain (Buerkle and Lexer 2008). In poplar, one of the
forest trees with rich genomic information, admixture mapping was
applied to various traits (Suarez-Gonzalez et al. 2018a; Bresadola et
al. 2019). Admixture mapping requires the inference of locus-specific
(local) ancestry, the number of alleles that originate from either
ancestral population involved in the admixture at individual loci
(Lindtke et al. 2013). Local ancestry usually deviates from genome-wide
ancestry of individuals, indicating the excess or deficit of admixture
at individual loci (Buerkle and Lexer 2008). A genome-wide pattern of
introgression is often illustrated using various approaches (Martin and
Van Belleghem 2017), for example, the Paterson’s D statistics
from the ABBA-BABA test that discriminates introgression from incomplete
lineage sorting (Martin et al. 2015). These approaches require a
sufficient number of genome-wide loci, which can be obtained from
sequences of reduced genomic libraries mapped to a whole-genome
reference sequence that has been available in white oaks (Plomion et al.
2018; Sork et al. 2022). Recently, reference sequences of Q.
mongolica var. mongolica and Qd also has been published
(Ai et al. 2022; Wang et al. 2023). Using genotypes, phenotypes, and
performance of trees admixed between Qc and Qd in common
gardens, we can verify adaptive introgression of Qd alleles at
loci associated with adaptive traits into Qc genome.
In this study, we tried to obtain evidence for the adaptive
introgression using inland and coastal common gardens (sites), where
seedlings of the focal white oak taxa, Qc , Qa , andQd , were planted from various provenances in Hokkaido and had now
reached about 30 years old. First, we examined their genetic variation
using genome-wide SNP genotypes to estimate genomic compositions of
hybrids and genome-wide patterns of introgression. Next, we measured
phenotypes of leaf and shoot traits and performance of trees in each
site to demonstrate adaptation of Qd -like phenotypes of these
traits to coastal environment. Finally, we searched for loci, at which
SNP genotypes and local ancestry were associated with those traits. We
expected that these trait-associated loci were located at introgressed
genomic regions and were close to genes involved in adaptation to
coastal environment.