The often patchy distribution of serpentine geology can lead to abrupt changes in soil and microclimates. Thus, serpentine areas provide an ideal natural setting to understand how divergent selection ...drives the process of local adaptation in edaphically specialized plants. When the serpentine ecotype is surrounded by a related nonserpentine ecotype, a balance of natural selection and potential gene flow should maintain the different ecotypes over very short distances. We aimed to reveal the mechanisms allowing soil ecotypes of a goldenrod species to co‐occur sympatrically in Japan.
We performed field surveys to characterize microenvironments and flowering phenology of each ecotype, common garden and reciprocal transplant experiments and artificial crossing, and population genetic analysis to investigate the levels of genetic differentiation between ecotypes.
Growth chamber experiments show that serpentine plants showed lower specific leaf area (SLA) and greater resource allocation to their root systems than did their nonserpentine counterparts, a potential adaptation to drier and less fertile soil condition in serpentine habitats. Reciprocal transplant studies demonstrated a clear pattern of local adaptation in the plant growth rate. Importantly, serpentine populations completed flowering by midsummer versus late summer in nonserpentine plants. This pattern is consistent with the hypothesis that early flowering ensures reproductive success, before the microclimatic conditions becomes severe in open habitats. Although prezygotic isolation was a strong barrier to gene flow, genetic differentiation was very low, indicating a recent origin for the serpentine ecotypes and/or gene flow at low frequencies.
Synthesis. The findings indicate that the early flowering times of serpentine ecotypes, which would have been selected for by microclimates in serpentine areas, can play roles in local adaptation, but also population isolation via a by‐product of diverged reproductive timings. This study contributes to general understanding of the initial stages of plant ecological speciation under potential gene flow in very small geographic scales.
Without any effective geographic barriers, the Solidago soil ecotypes were maintained by divergent selection imposed by microclimatic conditions in alternative habitats. Importantly, the divergent flowering time played dual roles of a local adaptation to each habitat and assortative mating to further restrict gene flow between populations.
Geranium erianthum
is an alpine plant growing in dry habitats, which is distributed from East Asia to northern coastal regions of the northern Pacific. The ice-free area around the current Bering ...Strait (i.e., Beringia) had played an important role in range expansion into neighboring regions such as East Asia and North America for some alpine plants. However, recent studies suggest that some alpine plants in snowbed environment spread from East Asia to northern coastal regions of the northern Pacific. In this study, we investigated phylogenetic relationships and genetic differentiations among populations of
G. erianthum
and the related species using the chloroplast genome and single-nucleotide polymorphisms, to evaluate the alternative biogeographic hypotheses in which region of Beringia, British Columbia or East Asia is probable for its distributional origin. Range reconstruction based on phylogenetic tree of chloroplast genome indicated
G. erianthum
and related species originated in East Asia, from where
G. erianthum
migrated eastward into Beringia and British Columbia. In addition, nuclear genome-wide SNPs indicated that no significant genetic differentiation was detected between Japanese and Beringian populations. The lack of genetic differentiation suggests that the current range of
G. erianthum
resulted from rapid range expansion during the latter period of the last glacial era. Overall, the East Asian refugium hypothesis was applicable to the alpine plant
G. erianthum
in dry habitat, indicating that range expansion pattern from East Asia into the northern Pacific may be more common rather than limited for snowbed species.
Lyric videos, or kinetic typography videos, are music videos showing lyric text in synchronization with the music. The purpose of this paper is to quantitatively and qualitatively analyze lyric ...videos to understand their design trends via three modalities: word motion, font style, and music style. These trends will not only be helpful as hints for designing new lyric videos but also be meaningful to quantitatively reveal the thought processes of the video design professionals. To achieve this, we needed to develop or utilize several technologies. First, we developed a lyric word tracking method to capture the motion of individual lyric words. The proposed method uses the lyric text as the guiding information for word tracking to overcome the difficulties arising from the various word appearances and motions. Second, we developed a font style estimator to quantify the appearance of each word as a feature vector. Finally, we employed a music style estimator to quantify the mood of the music, e.g., "techno" and "fast." We then analyzed feature vectors of these three style modalities collected at 3,494 time points in 100 lyric videos. After revealing the trend of each modality via k-means, we conducted a co-occurrence analysis to understand the correlation between each modality pair. Our experimental results indicate that such a cluster-wise co-occurrence analysis can capture interesting trends hidden in lyric video designs.
Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is ...effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.
Series Sakawanum (genus Asarum, Aristolochiaceae) comprises four taxa of forest understory herbaceous plants, which exhibits a geographical cline of calyx lobe length across taxonomic units. To ...understand the formation process of this series, it is necessary to investigate the evolutionary history based on maternally inherited seed-mediated plastid markers. Using pyrosequencing technique, nearly complete chloroplast genomes of two species (A. minamitanianum and A. costatum) were obtained. Furthermore, nine polymorphic chloroplast single nucleotide polymorphisms (SNPs) and 11 simple sequence repeat (SSR) markers were developed. Most of these markers showed interspecific variations and all markers showed transferability to other Asarum species, while most of markers showed little intra-population variations. These chloroplast genomes and markers can be applied in future studies investigating the contributions of the maternal lineage in shaping the population genetic structure of series Sakawanum and the evolutionary processes underlying their morphological diversification including the characteristic calyx lobe length variation. Moreover, this study showed the applicability of comparative chloroplast genome analysis to develop the chloroplast markers for species group for which it is difficult to obtain polymorphism data using the universal primers.
Interspecific hybridization is a critical issue in conservation biology because it may drive small populations to extinction through direct or indirect processes. In this study, to develop a ...conservation strategy for an endangered rear-edge population of Carex podogyna in Ashiu, Kyoto, Japan, we performed a molecular genetic analysis of the wild population and an ex-situ population established from wild seeds. Microsatellite genotypic data revealed a complete loss of genetic diversity in the wild population, suggesting that it has long been prone to genetic drift due to isolation as a small population. In contrast, microsatellite analysis of 13 ex-situ individuals detected multiple alleles that are not harbored in the wild C. podogyna population. Sequence analysis revealed that these individuals are likely natural hybrids between C. podogyna and a co-occurring species, C. curvicollis, although established hybrids have never been found in the natural habitat. Based on our observation of variegated leaves in hybrid individuals, we propose that hybrids have been excluded by natural selection and/or interspecific competition caused by insufficient productivity of photosynthesis, although other genetic and ecological factors may also be influential. Overall, this study indicates that natural mechanisms selectively removing the hybrids have maintained the genetic purity of this rear-edge population of C. podogyna, and also emphasizes the importance of genetic assessment in ex-situ conservation programs.
Poiret is a holoparasitic plant that lacks chlorophyll and totally depending on its host for its growth.
parasitizes host plant roots and extract nutrient and water via a haustorium. Although
...distributes in the Mediterranean region as a wild plant parasite, it parasitizes faba bean causing serious damages which may reach 90% yield losses in Tunisia. Analysis of genetic diversity of the parasite is important to better understand its evolution and spread, remained largely unknown. In this work, we present the first study on genetic diversity and population structure using the robust technique Restriction-site-Associated DNA sequencing (RADseq) for
spp. We collected 244 samples of
from 18 faba bean fields in the north of Tunisia including 17 populations from the north-west and one population form the north-east. To overcome the difficulty of SNP discovery in
genome as a non-model and tetraploid plant, we utilized three different informatics pipelines, namely UNEAK, pyRAD and Stacks. This study showed that genetic differentiation occurred in the Tunisian
emphasizing the isolation by distance effect. However, no strong population clustering was detected in this work basing on the three data sets and clustering methods used. The present study shed the light on the current distribution and the genetic variation situation of the fetid broomrape in Tunisia, highlighting the importance of understanding the evolution of this parasite and its genetic background. This will aid in developing efficient strategies to control this parasite and its expansion in Tunisia and worldwide.
Edaphic specialization is one of the main drivers of plant diversification and has multifaceted effects on population dynamics. Carex angustisquama is a sedge plant growing only on heavily acidified ...soil in solfatara fields, where only extremophytes can survive. Because of the lack of closely related species in similar habitats and its disjunct distribution, the species offers ideal settings to investigate the effects of adaptation to solfatara fields and of historical biogeography on the genetic consequences of plant edaphic specialization to solfatara fields. Here, genome‐wide single nucleotide polymorphisms were used to reveal the phylogenetic origin of C. angustisquama, and 16 expressed sequence tag–simple sequence repeat markers were employed to infer population demography of C angustisquama. Molecular phylogenetic analysis strongly indicated that C. angustisquama formed a monophyletic clade with Carex doenitzii, a species growing on nonacidified soil in the sympatric subalpine zone. The result of population genetic analysis showed that C. angustisquama has much lower genetic diversity than the sister species, and notably, all 16 loci were completely homozygous in most individuals of C. angustisquama. Approximate Bayesian computation analysis supported the model that assumed hierarchical declines of population size through its evolutionary sequence. We propose that the edaphic specialist in solfatara fields has newly attained the adaptation to solfatara fields in the process of speciation. Furthermore, we found evidence of a drastic reduction in genetic diversity in C. angustisquama, suggesting that the repeated founder effects associated with edaphic specialization and subsequent population demography lead to the loss of genetic diversity of this extremophyte in solfatara fields.
Premise of the study: Simple sequence repeat (SSR) markers were developed for Aster savatieri (Asteraceae) and the serpentine variety A. savatieri var. pygmaeus to re-evaluate their taxonomic status. ...Methods and Results: Using RNA-Seq data, 22 expressed sequence tag (EST)—SSR markers were developed. Polymorphisms were assessed in A. savatieri and in A.savatieri var. pygmaeus. The average number of alleles ranged from four to 15, and expected heterozygosity ranged from 0.417 to 0.870. Transferability was examined in six representative species of Japanese Aster and in Solidago virgaurea subsp. asiatica var. asiatica, a member of the tribe Astereae (Asteraceae); most of the loci were transferable to these examined species. Conclusions: These markers will be useful for genetic studies of variation in A. savatieri and other Aster species that occur in Japan.
Deer overabundance is a contributing factor in the degradation of plant communities and ecosystems worldwide. The management and conservation of the deer-affected ecosystems requires us to urgently ...grasp deer population trends and to identify the factors that affect them. In this study, we developed a Bayesian state-space model to estimate the population dynamics of sika deer (Cervus nippon) in a cool-temperate forest in Japan, where wolves (Canis lupus hodophilax) are extinct. The model was based on field data collected from block count surveys, road count surveys by vehicles, mortality surveys during the winter, and nuisance control for 12 years (2007-2018). We clarified the seasonal and annual fluctuation of the deer population. We found a peak of deer abundance (2010) over 12 years. In 2011 the estimated deer abundance decreased drastically and has remained at a low level then. The deer abundance gradually increased from April to December during 2013-2018. The seasonal fluctuation we detected could reflect the seasonal migration pattern of deer and the population recruitment through fawn births in early summer. In our model, snowfall accumulation, which can be a lethal factor for deer, may have slightly affected their mortality during the winter. Although we could not detect a direct effect of snow on population dynamics, snowfall decrease due to global warming may decelerate the winter migration of deer; subsequently, deer staying on-site may intensively forage evergreen perennial plants during the winter season. The nuisance control affected population dynamics. Even in wildlife protection areas and national parks where hunting is regulated, nuisance control could be effective in buffering the effect of deer browsing on forest ecosystems.
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