Adaptive radiation of the Callicarpa genus in the Bonin Islands
revealed through double-digest restriction site–associated DNA
sequencing analysis
Suzuki SETSUKO1, Satoshi NARITA2,
Ichiro TAMAKI3, Kyoko SUGAI4,
Atsushi J NAGANO5,6, Tokuko
UJINO-IHARA1, Hidetoshi KATO7, Yuji
ISAGI2
1Department of Forest Molecular Genetics and
Biotechnology, Forestry and Forest Products Research Institute, Forest
Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki,
305-8786, Japan
2Graduate School of Agriculture, Kyoto University,
Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan,
3Gifu Academy of Forest Science and Culture, 88 Sodai,
Mino, Gifu, 501-3714, Japan
4Institute of Agricultural and Life Sciences, Academic
Assembly, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane,
690-8504, Japan
5Faculty of Agriculture, Ryukoku University, 1-5
Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
6Institute for Advanced Biosciences, Keio University,
403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
7Makino Herbarium, Tokyo Metropolitan University, 1-1
Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
Running title: Adaptive radiation in Callicarpa
*Correspondence; Suzuki Setsuko, E-mail:setsukos@affrc.go.jp
ORCID Suzuki Setsuko, 0000-0002-0612-1853; Kyoko Sugai,
0000-0003-2426-6156; Ichiro Tamaki, 0000-0003-2315-243X; Atsushi J.
Nagano, 0000-0001-7891-5049; Tokuko Ujino-Ihara, 0000-0002-9243-1638;
Yuji Isagi, 0000-0002-9777-076X
ABSTRACT
The Bonin Islands, comprising of the Mukojima, Chichijima, and Hahajima
Islands, are known for their isolated and distinctive habitats, hosting
a diverse array of endemic flora and fauna. In these islands, adaptive
radiation has played a remarkable role in speciation, particularly
evident in the Callicarpa genus that is represented by three
species: Callicarpa parvifolia and Callicarpa glabraexclusive to the Chichijima Islands, and Callicarpa subpubescens ,
distributed across the entire Bonin Islands. Notably, C.
subpubescens exhibits multiple ecotypes, differing in leaf hair
density, flowering time, and tree size. In this study, we used
double-digest restriction site–associated DNA sequencing to analyze
species, ecotypes and geographical variations within Callicarpain the Bonin Islands. We aimed to determine detailed phylogenetic
relationships, investigate species and ecotype diversification patterns,
estimate divergence times, and explore cryptic species using genetic and
phenotypic data. Genetic analysis revealed that C. parvifolia andC. glabra formed a single, distinct genetic groups. Conversely,C. subpubescens showed seven genetic groups corresponding to
different ecotypes and regions, with one ecotype derived from the
hybridization of two others. Phylogenetic and population demography
analyses, focusing on six Chichijima and Hahajima Islands–based
species/ecotypes, indicated the divergence of an ecotype adapted to tall
mesic forests approximately 170 kya, whereas the other five
species/ecotypes diverged nearly simultaneously around 73–77 kya.
Environmental changes during the glacial period likely contributed to
this process of adaptive radiation. Moreover, leaf morphology, flowering
time, and genetic analyses suggested the presence of two cryptic species
within C. subpubescens .
Key words: ddRAD-Seq, Lamiaceae, Oceanic islands, Quaternary, Ogasawara
Islands
INTRODUCTION
Oceanic islands are geographically isolated—never been connected to
large landmasses. Owing to their distinctive characteristics and limited
colonization opportunities, the biotas of oceanic islands exhibit a
greater degree of endemic flora and fauna, often resulting from frequent
ecological speciation and adaptive radiation (Gillespie et al., 2001;
Givnish, 1997). Adaptive radiation refers to the rapid diversification
of lineages into multiple taxa, each adapted to distinct ecological
niches (Rundle & Nosil, 2005; Schluter, 2000). Some examples include
Darwin’s finches in the Galapagos Islands (Grant, 1986; Grant, 1998;
Grant & Grant, 2007) and silverswords and Hawaiian lobeliads in the
Hawaiian Islands (Carlquist et al., 2003; Givnish et al., 2009).
The Bonin Islands, comprising of the Mukojima, Chichijima, and Hahajima
Islands, are oceanic islands located approximately 1,000 km south of
Tokyo, Japan (Fig. S1). Despite their smaller land area (70
km2) and lower altitude (463 m) compared with other
oceanic islands, such as the Canary Islands (area, 7,490
km2; elevation, 3,718 m) and the Galapagos Islands
(area, 7,870 km2; 1707 m), the Bonin Islands exhibit a
high proportion of endemic vascular flora, with ~43% of
species being endemic (Ono et al., 1986), exceeding 26% and 43%
endemism in the Canary Islands (Aedo et al., 2013) and the Galapagos
Islands (Porter, 1978), respectively. Diverse habitats, including
forests, grasslands, and coastal areas, providing varied microclimates
and supporting multifarious plant species, coupled with the islands’
isolation, have facilitated the evolution of endemic species adapted to
specific ecological conditions in the Bonin Islands. The role of
adaptive radiation in driving the notable endemism rate of the Bonin
Islands is underscored by various genera, such as Crepidiastrum(Ito & Ono, 1990), Symplocos (Soejima et al., 1994), andPittosporum (Ito et al., 1997), which have experienced
diversification yielding three to four species each.
In the Bonin Islands, the genus Callicarpa is another example of
adaptive radiation (Ono, 1991; Shimizu & Tabata, 1991). Comprising
three endemic species, Callicarpa parvifolia , Callicarpa
glabra , and Callicarpa subpubescens . Callicarpa
parvifolia and C. glabra are restricted to the Chichijima
Islands, whereas C. subpubescens exhibits a wider distribution
across the Mukojima and Hahajima Islands (Fig. S1). Using microsatellite
markers, Sugai et al. (2019) demonstrated genetic differentiation among
the three Callicarpa species in the Chichijima Islands, as well
as multiple genetic groups within C. subpubescens in the Mukojima
and Hahajima Islands. Furthermore, Setsuko et al. (2023) identified four
ecotypes in the Hahajima Islands, one derived from hybridization of two
other ecotypes, with these ecotypes found to be locally adapted to soil
moisture and light conditions. However, detailed phylogenetic
relationships, as well as species/ecotype diversification timing and
order remain unclear. By examining differentiation patterns and
divergence time, it may be possible to infer how plants in the oceanic
islands diversified with geohistorical and/or environmental changes
(Kadereit & Abbott, 2021).
In this study, we aimed to elucidate detailed phylogenetic relationships
within the Callicarpa genus in the Bonin Islands, determine
species and ecotype diversification patterns, estimate divergence times,
and investigate cryptic species. To achieve these objectives, we
employed double-digest restriction site–associated DNA sequencing
(ddRAD-Seq), a genomic approach for detecting a large number of single
nucleotide polymorphisms (SNPs) throughout the genome. Known for high
resolution, ddRAD-Seq is suitable for investigating intricate
phylogenetic relationships within closely related taxa (Wagner et al.,
2013). The results of this study will offer fundamental insights into
the evolutionary history of Callicarpa in the Bonin Islands,
contribute essential knowledge on factors influencing species
diversification in island ecosystems, and enhance our understanding of
speciation processes. Moreover, the identification of potential cryptic
species highlights the importance of comprehensive genetic analyses in
biodiversity studies.
MATERIALS AND METHODS