Arabis alpina: a perennial model plant for ecological
genomics and life-history evolution
Stefan Wötzel t Institute of Ecology,
Evolution and Diversity, Goethe University Frankfurt and Senckenberg
Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
Marco Andrello t Institute for the study of
Anthropic Impacts and Sustainability in the marine environment, National
Research Council (CNR-IAS), Rome, Italy.
Maria C. Albani Institute for Plant Sciences, University of
Cologne, Cologne, Germany
Marcus A. Koch Biodiversity and Plant Systematics, Centre for
Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
George Coupland Dept. of Plant Dev. Biology, MPI for Plant
Breeding Research, Cologne, Germany
Felix Gugerli WSL Swiss Federal Research Institute,
Birmensdorf, Switzerland
t these authors have contributed equally to the
manuscript and should be considered as first authors
Correspondence: Felix Gugerli, Biodiversity and Conservation
Biology, WSL Swiss Federal Research Institute, Zürcherstrasse 111,
CH–8903 Birmensdorf, Switzerland. Email: felix.gugerli@wsl.ch
Running head : Ecological genomics of Arabis alpina
Abstract
Many model organisms have obtained a prominent status due to an
advantageous combination of their life-history characteristics, genetic
properties and also practical considerations. In non-crop plants,Arabidopsis thaliana is the most renowned model and has been used
as study system to elucidate numerous biological processes at the
molecular level. Once a complete genome sequence was available, research
has markedly accelerated and further established A. thaliana as
the reference to stimulate studies in other species with different
biology. Within the Brassicaceae family, the arctic-alpine perennialArabis alpina has become a model complementary to A.
thaliana to study life-history evolution and ecological genomics in
harsh environments. In this review, we provide an overview of the
properties that facilitated the rapid emergence of A. alpina as a
plant model. We summarize the evolutionary history of A. alpina ,
including the diversification of its mating system, and discuss recent
progress in the molecular dissection of developmental traits that are
related to its perennial life history and environmental adaptation. We
indicate open questions from which future research might be developed in
other Brassicaceae species or more distantly related plant families.
arctic-alpine environment, Brassicaceae, functional experiments,
gene–environment associations, local adaptation, perennial
1 |
INTRODUCTION
Describing and understanding the overwhelming diversity of life forms
depends on the establishment of model species as common study platforms.
By focusing on a single organism with practical advantages, a wealth of
knowledge can be generated. This has led to tremendous advances in the
understanding of fundamental principles in many disciplines of biology
(reviewed e.g. in Müller & Grossniklaus, 2010). In plant sciences,Arabidopsis thaliana has served as a widely used model for
several decades (Weigel, 2012). It combines many key characteristics of
a successful plant model: short life cycle, wide distribution, variation
in life-history traits, self-compatibility, small genome size, genetic
tractability, facile transformation and ease of cultivation. However, no
model can cover all areas of biological interest. Consequently, the
number of dedicated plant model species has increased continuously
(Cesarino et al., 2020; Kane et al., 2013; Koenig & Weigel, 2015),
which will benefit future research in many fields (Pyhäjärvi & Mattila,
2021).
For reasons of comparability, specific topics were initially addressed
using sister species from within the genus Arabidopsis .Arabidopsis halleri , for example, contributed to understanding
the molecular basis of heavy-metal tolerance (Hanikenne et al., 2008),
and has been developed into a perennial model system for population
ecology and adaptation (reviewed in Honjo & Kudoh, 2019).Arabidopsis arenosa originally served as a model for polyploidy
associated with hybridization (Monnahan et al., 2019; Yant & Bomblies,
2017), and more recently for evolutionary ecological genomics (Kolář et
al., 2016). Arabidopsis lyrata has attracted attention for
studies on mating system shifts (Mable, Dart, Berardo, & Witham, 2005),
phylogeography (Schmickl, Jørgensen, Brysting, & Koch, 2010),
adaptation (Kemi et al., 2013) and population genomics (Hämälä &
Savolainen, 2019). Similarly, more distantly related Cardamine
hirsuta has been used to study compound leaf development and seed
dispersal (Hay et al., 2014).
The fact that most of the species mentioned above are studied more
broadly today might indicate a change of paradigm in plant sciences. For
species with sufficient knowledge on mechanistic underpinnings, and
where increasingly powerful analytical methods are available, studies
can address more systemic questions such as trait evolution or
developmental biology in relation to environmental variation. Here, and
particularly in the study of closely related species, A. thalianaserves as reference to identify, for example, gene orthologs and address
gene function in phylogenetically closely related species that vary for
a trait of interest. The knowledge gained with A. thaliana and
its relatives is also extremely valuable when performing comparative
studies on even distantly related species.
Arabis alpina L. (Brassicaceae), the Alpine Rockcress, has
emerged as a model species for ecological genetics and life-history
evolution during the past fifteen years. Research on A. alpinastarted nearly 60 years ago with taxonomic studies by Hedberg (1962),
who compared populations from Africa and Scandinavia. About 50 years
later, phylogeographic studies inferred the species’ Pleistocene and
postglacial history (Ehrich et al., 2007; Koch et al., 2006), and
experimental studies highlighted that the differential breakdown of
self-incompatibility has led to populations with varying degrees of
self-compatibility (Ansell, Grundmann, Russell, Schneider, & Vogel,
2008; Tedder et al., 2015).
Arabis alpina is diploid with a base chromosome number ofn =8, and its karyotype resembles the putative ancestral state of
the Brassicaceae, which is in contrast to its Arabidopsisrelatives with n =5. The species can equally be genetically
manipulated by Agrobacterium- mediated transformation and, hence,
is amenable to the toolkit of molecular biology. Consequently, the
species has developed into a model system for addressing the molecular
mechanisms of perenniality (R. Wang et al., 2009). With the release of a
first reference genome assembly (Willing et al., 2015), comparative
genomic analyses have become possible, and similar to the development in
the genus Arabidopsis , studies have widened to include other
species from the genus Arabis (e.g. Kiefer et al., 2017).
The arctic-alpine Arabis alpina has a wide geographic
distribution in the European Alps, Spain, Arabia, East Africa, and
extends into Scandinavia, southern Greenland and northern parts of North
America (cf. Ansell et al., 2011; cf. Figure 1). Corresponding to its
broad range, habitats of A. alpina span a wide ecological
amplitude and elevation. Typically, plants occur on calcareous scree
slopes and rocky debris, where they can persist by elongating shoots
between the unstable substrate. However, individuals also thrive in more
sheltered areas where nutrients often accumulate due to dung deposition
of cattle, wild ungulates or birds, and they can tolerate very moist
conditions in moss-dominated communities along creeks or ravines (Figure
1). Many of these habitats are transient and can restrict the lifespan
of individual plants, which exemplifies the need for a developmental
flexibility. Given its wide distribution and broad ecological niche,A. alpina complements the aforementioned model species by
expanding into the extremes of plant occurrence, both in latitude and
elevation.
Here, we provide an overview of current knowledge on A. alpinaand introduce the various types of resources recently developed. We
summarize the species’ phylogeographic and evolutionary systematic
history and discuss its use as a model for studies of adaptation, mating
system evolution and the dissection of complex developmental traits.
Moreover, we include the latest progress in understanding its perennial
life history under natural conditions and the molecular and
physiological underpinnings of it, and finally provide perspectives on
potential future research.
FIGURE 1 HERE
2 |
EVOLUTION, SYSTEMATICS AND PHYLOGEOGRAPHY
Tribe Arabideae, which includes A. alpina , is one of the most
prominent tribes within the Brassicaceae family. It is a monophyletic
assemblage with roughly 545 species distributed among 18 accepted
genera, and convergence of morphological traits and trait complexes is
found in all main lineages (Walden, German, et al., 2020). Based on
recent cytogenetic evidence, Arabideae has been considered one of the
early emerging tribes among the evolutionary lineages described in
Brassicaceae, that is likely basal to all lineages except Aethionemeae
(Walden, Nguyen, Mandáková, Lysak, & Schranz, 2020). However, this
finding contradicts phylogenomic analyses (e.g. Kiefer et al., 2019;
Mabry et al., 2020; Nikolov et al., 2019; Walden, German, et al., 2020)
that placed the tribe close to Brassicaceae evolutionary lineage II (Box
1, Figure A-A). Despite this uncertainty, stem group and crown group
ages of the tribe can be roughly estimated at 20 mya and 18 mya,
respectively (Huang, German, & Koch, 2020; Walden, German, et al.,
2020).
Genus Arabis , which forms the core of tribe Arabideae, is a
well-studied para- and polyphyletic set of approximately 100 species
(Karl & Koch, 2013), for which A. alpina serves as the type
species. However, the genus at present does not form a monophyletic
group and will likely undergo further taxonomic revision. Even among the
taxa currently considered as closely related, including A.
caucasica that is often used as ornamental plant, there is ample
taxonomic uncertainty that still requires to be resolved. Nevertheless,
this taxonomic group encloses species with a great variety of
life-history characteristics that may serve as comparative study
systems. A detailed account of the systematic and taxonomic state of
knowledge—and uncertainty—is given in Box 1.
BOX 1 HERE
Phylogeographic studies on chloroplast and nuclear DNA indicate thatA. alpina originated in Anatolia. Present-day distribution was
established with three ancestral lineages (Ansell et al., 2011; Koch et
al., 2006) that diverged about 2-2.7 million years ago, at the
Pliocene–Pleistocene transition. This period was marked by rapid
cooling (Webb & Bartlein, 1992) and the expansion of habitats suitable
for alpine plants. During the Pleistocene, a fragmented network of local
survival centres persisted in Anatolia, possibly undergoing local
elevational migrations during fluctuations between warmer interglacial
and colder glacial periods (Ansell et al., 2011).
From Anatolia, a first lineage migrated to the Caucasus and the Iranian
Plateau through the Anatolian diagonal. This high-elevation mountain
system likely provided stepping-stone habitats for A. alpina to
eventually reach the East African high mountains (Ansell et al., 2011;
Koch et al., 2006). Within this lineage, the populations of the
Anti-Taurus and Mount Lebanon ranges form an independent clade (Ansell
et al., 2011). A second, more southern lineage formed two
phylogeographic groups in Ethiopia, which likely resulted from
previously isolated populations that came into secondary contact with
the East African lineage (Assefa, Ehrich, Taberlet, Nemomissa, &
Brochmann, 2007; Koch et al., 2006). From Western Anatolia, a third
lineage gave rise to all central and northern European populations
through multiple immigration events, and also served as a source for the
populations in Northwest Africa (Koch et al., 2006). Migration to Europe
probably occurred through the region around the Sea of Marmara during
colder glacial periods, when alpine habitats were located at lower
elevations (Ansell et al., 2011). Within this third lineage, populations
of A. alpina in the Alps and the Carpathians show high levels of
overall genetic diversity and form a mosaic of differentiated groups
with an East–West spatial structure (Alvarez et al., 2009; Ehrich et
al., 2007). This pattern might result from multiple recolonizations from
different refugia around and possibly within the Alps, the Carpathians
and the Tatras (Ansell et al., 2008; Ehrich et al., 2007; Rogivue, Graf,
Parisod, Holderegger, & Gugerli, 2018).
In more remote regions with milder climate, such as the Pyrenees and the
Mediterranean, A. alpina might have persisted in situduring glacial periods (Ehrich et al., 2007). Northern European and
North-American populations, by contrast, show very low levels of genetic
diversity (Ehrich et al., 2007). The authors propose colonization from a
single refugium in Europe. However, this scenario appears unlikely given
the vast periglacial area that expanded from the northern edge of the
Alps to the northern European glaciers. Alternatively, multiple
migrations with strong selection for colonization ability might have led
to a selective sweep decreasing genomic diversity (Ehrich et al., 2007).
Detailed knowledge on the spatial genetic structure and the underlying
demographic history is a valuable foundation for investigating
hypothesis-driven questions in ecological genetics. Likewise, knowledge
of the neutral genetic structure is essential when inferring signatures
of selection, because genomic imprints of past demographic processes
such as genetic drift may mimic selective processes at neutral loci.
Corresponding analyses require solid genomic resources, and a major step
in this direction was the establishment of a high-quality reference
genome for A. alpina , as described below.
3 |
REFERENCE GENOME AND APPLICATIONS
With 475 Mbp, the genome of A. alpina is roughly 3.5 times the
size of that of A. thaliana (Willing et al., 2015). This
difference in genome size largely relates to the accumulation of
retrotransposons in both hetero- and euchromatic regions of the genome,
exceeding that of other Brassicaceae species (Willing et al., 2015).
Usually, transposable elements are not randomly distributed across the
genome, but often accumulate within pericentromeric regions (e.g. The
Arabidopsis Genome Initiative, 2000). In A. alpina , an
evolutionarily recent transposition burst of Gypsy elements has
led to the expansion of pericentromeric regions and, consequently, about
half of the gene space of A. alpina is contained in the
heterochromatic compartment of the chromosome. By contrast, only a few
genes are located in the short pericentromeres of A. thaliana(Willing et al., 2015).
Pericentromeric regions can be characterized by low meiotic
recombination rates; hence, expansion of pericentromeric regions can
alter the recombination landscape (Tanksley et al., 1992). Transposon
density was shown to be correlated with patterns of linkage
disequilibrium along all chromosomes in natural A. alpinapopulations within the Swiss Alps, and a large proportion of the linked
blocks showed signatures of selective sweeps; those regions were
enriched for genes that are underlying adaptive traits, which implies
that transposon-mediated genome dynamics play a key role in natural
selection (Choudhury, Rogivue, Gugerli, & Parisod, 2019). Such genomic
features might complicate future genetic mapping experiments, which
depend on breaking up linkage groups to identify causal polymorphisms
that underlie signatures of selection.
The most recent release of the reference genome and other resources can
be accessed atwww.arabis-alpina.org (Jiao
et al., 2017). Subsequent re-sequencing of 35 and 304 individuals from
across the species range (Laenen et al., 2018) and the western Swiss
Alps (Rogivue et al., 2019) represented outstanding sequencing efforts
of natural plant populations, and the publicly available data offer
ample opportunities for in-depth population genomic analyses. Additional
genomic resources for A. alpina include the whole-chloroplast
genome sequence (Melodelima & Lobréaux, 2013) and a more fragmented
reference genome assembly using individual and pooled-sample sequencing
of a Swiss population (Rellstab et al., 2020). Future studies might
benefit from further, phylogenetically structured resources. For
example, tetraploidy of A. nordmanniana , which is the perennial
sister species of A. alpina, and the much smaller genome ofA. montbretiana (Kiefer et al., 2017), which is the annual sister
of A. alpina , suggests that other species from tribe Arabideae
could be used to study genome evolution. Only recently, phylogenetic
coverage has been expanded by studying genomic properties of A.
sagittata and A. nemorensis, illustrating how genomic resources
can allow for interspecific comparisons and eventually assist
conservation efforts (Dittberner et al., 2019).
4 |
MATING SYSTEM EVOLUTION
Understanding the processes governing mating-system evolution is
pivotal, because the mating system influences the distribution of
genetic diversity (Hamrick & Godt, 1996) and, thus, opportunities for
adaptive evolution (Charlesworth, 2006; Hartfield, Bataillon, & Glémin,
2017). One ubiquitous pattern among angiosperm plants is the repeated
transition to self-compatibility and increased selfing (Barrett, 2002),
which is commonly observed also in Brassicaceae (Mable, 2008).
Similar to Arabidopsis , A. alpina has a sporophytic
self-incompatibility system that partially has lost its function
(Tedder, Ansell, Lao, Vogel, & Mable, 2011) resulting in fully
outcrossing, fully selfing, but also mixed-mating populations. Hence,A. alpina offers a suitable platform for studying mating-system
variation within an evolutionary lineage. Until now, such studies have
been done at the interspecific level ( e.g. Capsella spp.;
Bachmann et al., 2019), but only few have targeted mating-system
variation within species ( e.g. A. halleri ; Griffin & Willi,
2014).
Comparative approaches have shown differences in flower morphology
between outcrossing and selfing populations, with the latter ones having
e.g. markedly smaller flowers and lower pollen production (Tedder et
al., 2015). Moreover, subtle differences in stigma–anther distance and
anther orientation translated into differential pollination success
between largely selfing populations from Scandinavia, France and Spain
(Toräng et al., 2017). On a local scale in the Swiss Alps, Buehler,
Graf, Holderegger, & Gugerli (2012) found evidence for mixed mating,
but inbreeding was predominant with 84% of collected seeds originating
from selfing. Nevertheless, these paternity analyses indicated effective
mating events over distances up to 1 km.
Based on F IS values, Ansell et al. (2008)
suggested that, after postglacial recolonization from southern Italian
refugia, self-incompatibility was lost when the species reached the
Alps, which was subsequently confirmed by pollination trials (Tedder et
al., 2011). Such a loss of self-incompatibility might assure
reproduction when chances for mating are restricted, e.g. during
migration. However, negative consequences of selfing, such as inbreeding
depression, might counterbalance this advantage. In a field experiment
in Scandinavia, Toräng et al. (2017) showed that the capacity for
self-pollination conveyed a fitness advantage in the pollinator-poor
tundra, leading to selection for flowers with more introrse anthers and
reduced anther–stigma distance. This observation may imply that
detrimental alleles, potentially inducing inbreeding depression, had
been purged in Scandinavian populations. However, Laenen et al. (2018)
could not substantiate this: by using genome resequencing data, they
demonstrated that Scandinavian populations had strongly reduced genetic
diversity and increased genetic load resulting from increased selfing
and a strong bottleneck, likely associated with post-glacial
recolonization. By contrast, genetic diversity and load of mixed-mating
French and Spanish populations were similar to the obligate outcrossing
Italian and Greek populations, suggesting a reduced cost of
self-compatibility in mixed-mating populations (Laenen et al., 2018).
Information on the causes and consequences of varying mating systems
eventually will help evaluate how A. alpina may cope with
environmental changes, e.g. due to climate warming. A local population
may increase its persistence by pollinator-independent reproduction
including asexual growth, in combination with phenotypic plasticity, or
through spreading potentially beneficial alleles by pollen and seed.
Here, newly arising mutations or standing genetic variation may form the
basis for local adaptation. The latter has become a prime topic in
evolutionary research, including a series of early studies involvingA. alpina, as outlined in the following section.
5 |
ADAPTATION TO ARCTIC AND ALPINE ENVIRONMENTS
Alpine environments are ideal settings for studies on local adaptation
due to large habitat diversity over short distances (Scherrer & Körner,
2011), and patterns of differentiation were found in alpine plants along
geographically narrow gradients (Byars, Papst, & Hoffmann, 2007; Kim &
Donohue, 2013; Leempoel, Parisod, Geiser, & Joost, 2018). The broad
distribution of A. alpina offers many opportunities to
investigate adaptive processes at different spatial scales. Habitats
located on a latitudinal gradient from the Alps to Scandinavia are
expected to share typical features, such as a low annual mean
temperature and a short growing season, while photoperiod length, but
also light intensity, is strongly differentiated. Habitats located in
the Cantabrian mountains, the Pyrenees, the Central Alps and the
Carpathian Mountains share aspects of alpine habitats, but differ in the
degree of continentality. These clines can be exploited to test for
broad-scale natural variation in A. alpina . Moreover, local
surveys can be replicated to test for convergent evolution or the
contribution of biogeographic history to local adaptation. Consequently,A. alpina has been extensively used for studies on local
adaptation and has become a showcase for landscape genomic analyses.
5.1 |
Experimental approaches: reciprocal transplantations and common gardens
In a classical long-distance reciprocal transplantation experiment,
strong local adaptation was detected between populations from the
Spanish and Scandinavian edges of the European range of A. alpina(Toräng et al., 2015). At both transplantation sites, fitness parameters
were consistently higher for local than for foreign provenances
(sensu Kawecki & Ebert, 2004), while differences between
regional replicate populations were negligible. This suggested
adaptation towards large-scale habitat differences, such as winter
minimum temperature, which was lower in Scandinavia than in its southern
counterpart, and the intensity of summer drought, which was more
pronounced in Spain than in the North. Both temperature and
precipitation were previously identified as key environmental parameters
shaping adaptive differentiation in plants and animals across the globe
(Siepielski et al., 2017), in several alpine plant species (Manel et
al., 2012) and also in A. alpina within the European Alps (e.g.
Manel, Poncet, Legendre, Gugerli, & Holderegger, 2010).
Significant signatures of local adaptation were also detected on a
regional scale within the French Alps (de Villemereuil, Mouterde,
Gaggiotti, & Till-Bottraud, 2018). A comparison of plants from six
populations in two different mountain ranges in common gardens close to
the natural sites revealed phenotypic differentiation in traits related
to vegetative and reproductive performance. Again, temperature was the
key environmental parameter explaining the observed patterns: Plants
originating from low-elevation sites grew more vigorously and had higher
reproductive output than those from high-elevation populations, which
may relate to respective higher average temperatures and longer growing
seasons.
In the study of de Villemereuil et al. (2018), the degree of phenotypic
plasticity depended on the population of origin, with plants from higher
elevations showing less plasticity for the measured traits, suggesting
another layer of adaptation to contrasting environments. Phenotypic
plasticity was also detected in the comparison of Scandinavian and
Spanish accessions (Toräng et al., 2015): the onset of flowering
differed markedly between local and foreign populations at the
Scandinavian, but not so much at the Spanish site. Hence, it is likely
that adaptation on both the large and regional scales includes specific
cues that are only partially fulfilled in the foreign transplantation
site. Given the latitudinal distance between Spain and Scandinavia, it
might be expected that temperature interacts with photoperiod to
synchronize flowering phenology with regional conditions (King & Heide,
2009).
The mentioned studies on local adaptation in A. alpina focused on
abiotic drivers and traits that show variation in relation to
latitudinal and elevational contrasts. Buckley, Widmer, Mescher, & De
Moraes (2019) also considered elevational clines, but combined field
observations and climate chamber experiments using populations ofA. alpina to investigate variation in traits related to growth
and herbivore defence. In this yet single study including biotic drivers
of adaptation, the authors found a link between herbivore pressure, leaf
traits and defence compounds, which they associated to growth–defence
phenotypes. Moreover, signals of adaptation were site-specific even
among populations located at the same elevation.
5.2 |
Landscape genomics
Earlier studies attempting to identify genomic signals of local
adaptation, commonly referred to as landscape genomics, relied on genome
scans using amplified fragment length polymorphisms (AFLPs). In A.
alpina, outlier AFLP loci, considered to be adaptive due to
significantly higher genetic differentiation than others, indicated
temperature and precipitation as the main environmental drivers of local
adaptation (Manel et al., 2010; Poncet et al., 2010; Zulliger, Schnyder,
& Gugerli, 2013). In two cases, such outlier loci were sequenced and
found to be located within gene regions: one matched the SIT4
phosphatase-associated family protein known from A. thaliana andA. lyrata (Buehler et al., 2013), and the other one was
homologous to a nucleotidyltransferase family protein in A.
thaliana (Zulliger et al., 2013). However, genotyping an independent
set of populations (Buehler, Brodbeck, Holderegger, Schnyder, &
Gugerli, 2014) could not confirm SIT4 variants to associate with
contrasting habitat types as in the original study, suggesting that
local adaptation to similar environmental cues may involve different
genes in different independent sets of populations (Rellstab et al.,
2017).
More recent studies made use of whole-genome sequencing data. A genome
scan based on reduced representation sequencing data identified a
candidate gene associated with growth performance in A. thaliana ,
which could explain the observed patterns in vegetative performance inA. alpina (de Villemereuil et al., 2018). Additional 19 genomic
regions associated with temperature, precipitation and snow cover
(Lobréaux, Manel, & Melodelima, 2014; Lobréaux & Miquel, 2020), and
these included orthologs of genes involved in abiotic stress response
and the regulation of flowering in A. thaliana . By increasing
both genomic and spatial resolution, Rogivue et al. (2019) identified
candidate SNPs for local adaptation to stress and defence response.
Interestingly, this study also identified transposable elements largely
shared among populations and corresponding to temperature response
terms.
In an alpine environment, similar environmental factors are relevant for
many plant species (Körner, 2003; Manel et al., 2012). It is hence
possible that selection targets the same genes or pathways in
phylogenetically distant species that occupy similar ecological niches
(Stern, 2013), even though this general assumption may not hold true
(see above). Two studies compared the genes involved in adaptation to
the Arctic environment in different species including A. alpinaand found that adaptation involved similar functional pathways, but most
adaptive genes remained species-specific (Birkeland, Gustafsson,
Brysting, Brochmann, & Nowak, 2020; Rellstab et al., 2020).
In summary, it appears that common environmental drivers, such as
temperature and precipitation, are associated with adaptive
differentiation in A. alpina . This might not be unexpected for an
arctic-alpine pioneer plant that has specific, but broad habitat
preferences. While most of the discussed regional and local findings
were uncovered within the French and Swiss parts of the European Alps,
it remains to be tested if similar patterns exist elsewhere, taking full
advantage of the broad distribution range of A. alpina and
including populations that have evolved within a tremendously different
environment
6 |
POPULATION DYNAMICS AND DEMOGRAPHY
Demographic dynamics of natural populations contribute to shaping and
partitioning natural variation within and among populations at the local
and regional scale. Over six years, Andrello et al. (2020) studied
demographic parameters (survival probability, growth variables,
reproduction probability, fecundity) of individuals in six natural sites
representing the species’ elevational range in the Alps. These authors
found mostly consistent values for mean annual survival probability
(S =0.5) and mean probability of reproduction
(F 0=0.5) across populations. Moreover,
demographic rates were related to environmental conditions in these
populations: Survival tended to increase, while growth and fecundity
tended to decrease with elevation. These findings in A. alpinareflect common patterns in life histories of herbaceous plants: Small,
long-lived species tend to inhabit high elevations, and vice-versa
(Laiolo & Obeso, 2017; Nobis & Schweingruber, 2013). Andrello et al.
(2020) also observed that individual A. alpina plants frequently
grew larger and produced more fruits when the surrounding vegetation was
composed of tall-growing species with large specific leaf areas. This
could indicate a response to competition with other plants or an effect
of temperature, because vegetative height and specific leaf area
commonly increase with temperature (Read, Moorhead, Swenson, Bailey, &
Sanders, 2014; Rosbakh, Römermann, & Poschlod, 2015).
Despite marked clines in demographic rates along elevation, A.
alpina showed surprisingly little variation in population growth rates
across its full elevational range (Andrello et al., 2020). This lack of
spatial variation in growth rates could be partly ascribed to
demographic compensation among different life-cycle components (Andrello
et al., 2020). In particular, increased survival probabilities at higher
elevation compensated for lower fecundity. Moreover, interannual
variation in survival probabilities, which reduces population growth
rates, was smaller at higher than at low elevation and further
contributed to compensation. Such negative correlations between
life-cycle components can result from opposite responses to shared
environmental drivers or from trade-offs between different life-cycle
processes (Knops, Koenig, & Carmen, 2007; Williams, Jacquemyn, Ochocki,
Brys, & Miller, 2015). In addition to showing little spatial variation,
population growth rates were all negative, suggesting that populations
are declining and might eventually go locally extinct. Accordingly, the
persistence of metapopulations of A. alpina depends on
recruitment from the seed bank and/or immigration from nearby sites.
However, strong genetic differentiation between the six studied
populations (F ST=0.6; de Villemereuil et al.,
2018) suggests low dispersal rates, and hence strong effects of genetic
drift likely combined with inbreeding through selfing. Conversely,
viable seeds of A. alpina were observed in the seed bank of
several arctic-alpine soils (Diemer & Prock, 1993; Philipp et al.,
2018), which can also be seen as a genetic legacy of former local
occurrences.
From such demographic observations, we can infer a differential
contribution of individual plant life-cycle components to population
persistence. The time at which any individual enters a particular stage
of its life cycle and the time it spends within that stage can vary
according to the prevalent environmental conditions and the genetic
composition of the individual. Hence, understanding the developmental
biology of traits that interact with demographic trajectories is
pivotal, as exemplified in the next section.
7 |
PERENNIAL GROWTH HABIT AND TRAIT EVOLUTION
Polycarpic plants such as A. alpina can flower and reproduce
several times during their lifetime, whereas monocarpic plants like the
classical plant model A. thaliana are commonly annual and
reproduce only once before they die (for details on modes of parity see
Hughes, 2017). One major difference between these two life strategies is
that senescence after flowering is restricted to reproductive branches
in polycarpic plants, whereas it is global in monocarpic plants. Within
the Brassicaceae, the transition from polycarpic to monocarpic life
history has occurred many times (Kiefer et al., 2017). It is now
possible to dissect the mechanisms that contribute to life-history
evolution at the molecular level using comparative studies betweenA. alpina and its annual relatives A. montbretiana andA. thaliana . Below, we showcase some important traits described
in A. alpina that contribute to the polycarpic perennial life
history.
FIGURE 2 HERE
7.1 |
Juvenile phase length
Physiological experiments under controlled environmental conditions have
demonstrated that seedlings of the Spanish A. alpinaPajares reference accession require a minimum of five weeks of
growth in long-day conditions before they are competent to respond to
flower inductive stimuli (R. Wang et al., 2011). The molecular
mechanisms regulating juvenile–adult phase change are similar to those
described in A. thaliana ; in both species, this trait is
regulated by the sequential action of two microRNAs, miR156 and miR172
(Wu et al., 2009). Typically, miR156 accumulates in the apices of young
seedlings and decreases as plants become older and reach reproductive
maturity, while at the same time levels of miR172 increases (Wu et al.,
2009). miR156 targets a family of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE
(SPL) transcription factors, whereas miR172 regulates a sub-clade of AP2
transcription factors which include APETALA2 (AP2) and the AP2-like
SCHLAFMÜTZE (SMZ), SCHNARCHZAPFEN (SNZ), TARGET OF EAT1-3 ( TOE1-3;
Aukerman & Sakai, 2003; J. W. Wang, Czech, & Weigel, 2009; Wu et al.,
2009). Orthologs of some of these genes have also been functionally
characterised in A. alpina and it has been demonstrated that they
contribute to the age-dependent control of flowering. These factors
include the A. alpina orthologs of SQUAMOSA
PROMOTER-BINDING PROTEIN-LIKE15 (AaSPL15 ), PERPETUAL
FLOWERING2 (PEP2 , the A. alpina ortholog of AP2 )
and TARGET OF EAT2 (AaTOE2 ; Bergonzi et al., 2013; Hyun et
al., 2019; Lazaro et al., 2019; Zhou, Gan, Viñegra de la Torre, Neumann,
& Albani, 2021).
Although the role of these genes in the age-pathway is conserved betweenA. thaliana and A. alpina , they additionally contribute to
the polycarpy of A. alpina, which maintains vegetative growth
after flowering (Table 1). For example, polycarpy is compromised inpep2 and toe2 mutants, and in transgenic lines that
express microRNA resistant forms of AaSPL15, in which all axillary
branches become reproductive (Table 1; Hyun et al., 2019; Lazaro et al.,
2019; Zhou et al., 2021). These additional roles of age-related factors
in polycarpic A. alpina may result from a more prominent role of
the age-pathway than in A. thaliana, in which the age-pathway
cannot be bypassed by other flowering-time pathways (Hyun, Richter, &
Coupland, 2017; Hyun et al., 2019).
7.2 |
Ecological significance of flowering behaviour
Cold is a major environmental factor that plants have to cope with, but
at the same time it provides a distinct cue for synchronizing flowering
with favourable environmental conditions. Arabis alpina requires
exposure to prolonged cold to flower, a process known as vernalization
in A. thaliana and other temperate perennials. Alpine
environments are characterised by long winters and unpredictably short
growing seasons, which puts additional constraints on alpine species.
Hence, many plants from alpine habitats initiate floral organs several
months or years before anthesis, so that they can flower rapidly once
environmental conditions are benign (Billings & Mooney, 1968; Diggle,
1997; Körner, 2003). In experimental conditions, flower buds are formed
during cultivation at 4°C (Lazaro, Obeng-Hinneh, & Albani, 2018; R.
Wang et al., 2009) and in natural populations of A. alpina ,
flower buds can already be observed in autumn (S. Wötzel, personal
observation), suggesting that A. alpina plants can be vernalized
and initiate flowering before winter. Experiments characterizing the
flowering response of the reference accession Pajares to
different durations of cold treatment indicated that exposure to less
than 12 weeks of cold leads to asynchronous flowering among individuals
and floral reversion, thereby reducing reproductive output (Lazaro et
al., 2018; R. Wang et al., 2009). These results suggest that natural
populations may require locale-specific cold periods for optimal
reproduction.
Flowering in response to long cold in A. alpina is mediated by
the MADS box transcription factor PERPETUAL FLOWERING 1 (PEP1; R. Wang
et al., 2009), which is the orthologue of the A. thalianaFLOWERING LOCUS C (FLC ; Michaels & Amasino, 1999;
Sheldon, Rouse, Finnegan, Peacock, & Dennis, 2000) . Similar toFLC , PEP1 acts as a floral repressor and is
transcriptionally regulated by vernalization. In A. alpina plants
of the reference accession (wild type), PEP1 transcript abundance
decreases during cold exposure and plants form flower buds (Lazaro et
al., 2018; R. Wang et al., 2009). In addition, pep1 mutants and
accessions with non-functional alleles of PEP1 (AaFLC) flower
early and without cold exposure (Albani et al., 2012; R. Wang et al.,
2009), resembling the early flowering phenotype of A. thalianaflc mutants (Michaels & Amasino, 1999).
Vernalization stably silences PEP1 only in mature meristems,
which initiate reproductive development during cold exposure, but not in
juvenile meristems, which remain vegetative (Lazaro et al., 2018). This
suggests that besides the age-pathway, differences in
vernalization-mediated PEP1 stable silencing by vernalization, as
observed between reproductive and vegetative meristems, may also
contribute to the polycarpic growth habit of A. alpina (Table 1;
reviewed in Soppe, Viñegra de la Torre, & Albani, 2021). PEP1mRNA levels are upregulated in meristems that did not commit to
flowering during vernalization to ensure the maintenance of vegetative
growth habit the following year (Lazaro et al., 2018; R. Wang et al.,
2009). This role of PEP1 may also pleiotropically contribute to maintain
dormant buds by ensuring the continuous supply of auxin from vegetative
axillary branches even after flowering (Soppe et al., 2021; Vayssières
et al., 2020). In common garden trials, accessions with non-functionalPEP1 alleles showed increased mortality, suggesting that PEP1
function is relevant for plant survival (Albani et al., 2012; Hughes,
Soppe, & Albani, 2019). This is probably related to the reduced
vegetative perseverance observed in pep1 mutants. In addition,
seed longevity and dormancy have been found to be reduced in pep1mutants (Table 1; Hughes et al., 2019), suggesting a potential shift
towards a rapid-cycling life strategy that closely resembles the
monocarpic growth habit.
Arabis alpina has also been used to study further developmental
traits (exemplified in Fig. 2), which include leaf trichome formation
(Chopra et al., 2019, 2014), leaf senescence (Wingler, Juvany, Cuthbert,
& Munné-Bosch, 2015; Wingler, Stangberg, Saxena Triambak, & Mistry,
2012), secondary growth (Sergeeva et al., 2021) and adventitious rooting
(Mishra, Roggen, Ljung, & Albani, 2020). For the latter, natural
variation has been detected under controlled environmental conditions
(Mishra et al., 2020). This finding might indicate a potential adaptive
significance for that trait, with different phenotypic optima for
individual populations. Observations in natural alpine environments
suggest that adventitious roots in A. alpina may primarily serve
for attaching the growing plant body to unstable substrate (Figure 1H),
an adaptation similar to those found in other scree-inhabiting plant
species (Körner, 2003).
In summary, comparative physiological studies between A. alpinaand A. thaliana , chemically induced mutants, functional studies
and the observation of natural accessions of A. alpina have
resulted in a detailed understanding of perennial life-history traits at
the molecular level. Many, if not all, of these traits may be of
adaptive significance, and the examples of flowering time and duration
have highlighted the crucial role of naturally occurring variants for
characterising gene functions. Future studies will be motivated by the
functional characterization of candidate loci that were identified by
landscape genomics methods (see above). In return,
molecular-physiological approaches can provide the proof-of-concept data
that is often the step remaining to be completed in contemporary studies
of adaptation. Further synergies might result from comparing trait
expression and gene function between annual and perennial life histories
within the Arabideae. Introgression lines of A. alpina that
contain genomic regions of the annual close relative A.
montbretiana in a common genetic background have been developed as a
tool to understand the divergence of annual and perennial life histories
(Hyun et al., 2019; Kiefer et al., 2017). It will be interesting to see
to which extent the relevant traits can be related back to the
environments in which the contrasting life histories have evolved.
8 |
PERSPECTIVES
In this overview, we demonstrate that A. alpina is well suited to
answer general questions related to the adaptation of plants to harsh
arctic-alpine environments and the evolution of perennial life-history.
However, there still are many unknowns that await to be addressed using
the wealth of available biological resources to expand current
knowledge. Here, we formulate some avenues that may guide future
research in the fields of ecological, evolutionary and molecular
genetics in A. alpina and other taxa.
Predominant selfing has been considered as a drawback for the study of
adaptation (Yant & Bomblies 2017), but the very availability of
outcrossing populations endorses A. alpina as a model for
studying mating system evolution within a single species.
Similarly, it can be tested whether inter specific differences in
life-history and functional traits (e.g. Adler et al., 2014; Nobis &
Schweingruber, 2013; Read et al., 2014) can be observed at theintra specific level. One could, for example, specifically address
adaptation to extreme environmental factors such as high irradiance, low
temperatures, persistent snow cover and short growing season: How
similar is the genomic basis of evolutionary solutions to these
ecological challenges in species that inhabit arctic and alpine
habitats? Do different strategies exist, are differences found within
the same genes or gene networks, or were complementary pathways involved
in these adaptive processes? What is the molecular basis of highly
specialized physiologies, such as the ability of the alpine snow-bed
specialist Soldanella pusilla to grow at freezing temperatures
(Körner et al., 2019)? Here, lessons learnt from an arctic-alpine model
system may help pinpointing the genomic particularities that also govern
physiological processes in other taxa (cf. Park, Kim, & Lee, 2017).
A broad variety of landscape genomic approaches and genome-wide studies
have identified polymorphisms within genes that are promising candidates
for being involved in adaptive processes. Future research might further
address the molecular genetic basis of ecologically relevant traits
besides the regulation of flowering, which is increasingly well
understood. There are still many traits that are relevant in view of
adaptation to arctic-alpine environments, in particular regarding biotic
stress such as pathogens and herbivory (but see Buckley et al., 2019).
Initial physiological studies have addressed response to cold stress and
detected clinal variation with increased frost tolerance at high
elevations, suggesting adaptive significance of that trait (Kolaksazov,
Ivanova, Stanev, Markovska, & Ananiev, 2017). A similar trajectory was
identified by Wingler et al. (2015), who found higher cold stress
tolerance in plants from high compared to low elevations, likely
mediated by higher leaf sucrose levels. However, at warmer temperatures,
sugar accumulation led to accelerated leaf senescence, suggesting a
physiological trade-off with frost protection shaping natural variation
(Wingler et al., 2012). Moreover, the physiology of storage metabolites
has been addressed in relation to secondary growth and perennial
behaviour (Sergeeva et al., 2021). However, there are yet further
eco-physiological studies needed to better understand the functional
aspects of adaptation to cold in A. alpina .
Environmental stress has been shown, e.g. in A. thaliana , to
induce enhanced activity of transposable elements (TEs), which in turn
affects gene integrity or the regulation of gene expression. Epigenetic
transmission can then lead to an acquired adaptive response in the next
generation (Thieme & Bucher, 2018; Thieme et al., 2017). At present, we
are unaware of any investigation that evaluates how epigenetic changes
(Richards et al., 2017) contribute to the ability of A. alpina to
cope with environmental stressors. Here, we see great potential in
establishing links between genome-wide methylation patterns and the
pertinent information on the types, activity and distribution of TEs
(Choudhury, Neuhaus, & Parisod, 2017; Choudhury et al., 2019).
Another key to the adaptive success of plants is their ability to
associate with mutualistic organisms. In many taxa, fungi or other
microbiota associate with plant roots to form close mutualistic
symbioses. To date, only limited information is available on howA. alpina may benefit from such root associates. For example,
Almario et al. (2017) characterized fungal microbiota on A.
alpina roots and found certain taxa to be dominant on soils with low
phosphorus content. Their results indicate microbial support for
phosphorus uptake under limiting conditions and suggest that taxa
growing on alpine, often nutrient-poor soils, can evolve alternative
solutions to the otherwise common mycorrhizal symbiosis. Nevertheless,
it remains unclear how common these associations are, whether they lead
to co-adaptations in the involved physiological pathways, and to which
degree they influence the evolutionary trajectory of the host plant.
Here, hypotheses could be developed in relation to the extended
phenotype concept (Gugerli et al., 2013; Whitham et al., 2006) and
tested using A. alpina .
While most of the aforementioned research is centred on populations from
the European Alps and the Spanish reference accession Pajares ,
future studies should expand along the phylogeography of A.
alpina . Accessions from the Anatolian mountains and African sky islands
might contain unexpected genetic variants underlying traits that provide
adaptation to a strongly divergent habitat. Particularly the equatorial
daytime climate, to which the African populations are exposed, radically
differs from the extreme seasonal habitats of Northern latitudes.
Moreover, analyses of such distinct lineages might change the
understanding of the species’ evolutionary history, similarly to what
has been shown for the example of A. thaliana after including
previously neglected accessions from Africa (Durvasula et al., 2017). It
is also possible that accessions from more southerly climates contain
genetic variants that may provide adaptive advantages for cold adapted
species that are threatened by global warming.
Biological discoveries can be expanded from A. alpina to closely
related sister species within the Arabideae, and to those in other
well-studied genera of the Brassicaceae such as Arabidopsis ,Capsella , Boechera, Cardamine and Brassica (Krämer,
2015; Rushworth, Song, Lee, & Mitchell-Olds, 2011). With more and more
plant species being fully sequenced, comparative genomics are becoming
increasingly feasible. Studies of such kind have just begun to address
principles of adaptation in the Brassicaceae (Birkeland et al., 2020;
Nowak et al., 2020; Rellstab et al., 2020) and provide opportunities for
understanding the adaptive evolution of life-history traits.
Taken together, widening the phylogenetic and environmental scales will
further help understanding fundamental processes in adaptation. The
marked variation in life-history traits encountered across the natural
range of A. alpina , together with the publicly available genomic
resources established in recent years, will serve as a comprehensive
basis for comparative studies. With this overview on the evolutionary
and ecological genomics of A. alpina , we demonstrate that this
species is a valuable emerging model system in plant biology. Together
with a suite of other taxa, A. alpina complements the hitherto
outstanding A. thaliana , on which a huge array of research is
still relying, to address complementary ways of evolutionary responses
to environmental cues. Additional, intensively studied taxa will enrich
the field of evolutionary plant biology and contribute to knowledge
about the manifold ways plants cope with their abiotic and biotic
environment.
ACKNOWLEDGEMENTS
The authors would like to thank all participants of a symposium onArabis alpina, hosted at the MPI for Plant Breeding Research
(Cologne, Germany) in 2018, for valuable discussion and contributions to
a meeting report stimulating this review. Christian Rellstab, Korbinian
Schneeberger and Irène Till-Bottraud provided helpful comments on an
earlier version of the article. MCA acknowledges the Cluster of
Excellence on Plant Sciences (CEPLAS) funded by the Deutsche
Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s
Excellence Strategy—EXC 2048/1—Project ID: 390686111. FG
acknowledges the inspiration for much of his Arabis research by
Pierre Taberlet and Rolf Holderegger, and financial support through the
Swiss National Science Foundation (GeneScale, CR32I3_149741).