Evolutionary history of Hemerocallis in Japan inferred from chloroplast and nuclear phylogenies and levels of interspecific gene flow

Hirota, Shun K.; Yasumoto, Akiko A.; Nitta, Kozue; Tagane, Misa; Miki, Nozomu; Suyama, Yoshihisa; Yahara, Tetsukazu

doi:10.1016/j.ympev.2021.107264

Cited by 17 publications

(12 citation statements)

References 79 publications

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“…In the current study, we found that dpMIG-seq libraries could be constructed using DNA extracted via a method lacking a purification step (Jia et al ., 2021), indicating that dpMIG-seq does not require high-quality DNA, an advantage of MIG-seq originally described by Suyama and Matsuki (2015). MIG-seq has been used in many ecological and taxonomic studies since its development (Cho et al ., 2021; Hirota et al ., 2021, 2022; Hoshino et al ., 2021; Nakajima et al ., 2021; van Ngoc et al ., 2021; Saito et al ., 2022; Toji et al ., 2022; Yahara et al ., 2021a, 2021b), although <1,000 SNPs were available in some studies (Table S10). As a novel method, dpMIG-seq may be useful as an alternative to conventional MIG-seq in future ecological and taxonomic studies that require an increased number of markers when clonal identification or species with small genomes are the target of analysis.…”

Section: Discussionmentioning

confidence: 99%

Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Nishimura

Kokaji

Motoki

et al. 2022

Preprint

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Multiplexed inter-simple sequence repeats genotyping by sequencing (MIG-seq) is an next-generation sequencing library construction method developed for the analysis of DNA in ecology. Although MIG-seq can generate libraries from low-quality DNA, few polymorphisms can be obtained in species with small genomes. In this study, we developed degenerate oligonucleotide primer MIG-seq (dpMIG-seq) as an effective polymorphism discovery method that allows for variation in the number of polymorphisms while retaining the advantages of MIG-seq, including independence from DNA quality. In dpMIG-seq, a proportion of the simple sequence repeats in the primer sequence of the first PCR in MIG-seq was changed to degenerate oligonucleotides to enable annealing to a wider range of sequences. In tests of several crop species other than wheat, the number of loci that could be sequenced using dpMIG-seq with a data volume of 0.3 gigabases (Gb) was increased compared with that sequenced using MIG-seq. In wheat, the number of polymorphisms obtained via dpMIG-seq was higher than that obtained via MIG-seq when a data volume of about ≥2 Gb was obtained. In dpMIG-seq, different loci could be sequenced by changing the positions of the degenerate oligonucleotides. By applying dpMIG-seq, we constructed a linkage map consisting of 5,142 markers for the rice inter-subspecies F2 population, and we detected quantitative trait loci for heading date in the regions where known heading-related genes were located. Overall, our results show that dpMIG-seq is a useful tool for the genetic analysis of crop species.

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Section: Discussionmentioning

confidence: 99%

Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Nishimura

Kokaji

Motoki

et al. 2022

Preprint

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“…Although previous studies have shown that some intraspecific clades are weakly associated with geography (Hirota et al, 2021; Murakami et al, 2020), no information is available on the genetic diversity and demographic changes of regional populations because these studies analysed only one or a few samples per population. To evaluate the contribution of genetic differentiation among regions and taxa, we performed a hierarchical analysis of molecular variance (Excoffier et al, 1992).…”

Section: Methodsmentioning

confidence: 99%

“…exaltata (insular taxon in Tobishima and Sado Islands). Previous genetic studies of H. middendorffii were performed to reveal phylogenetic relationships between H. middendorffii populations, using universal molecular markers, such as chloroplast DNA (Noguchi et al, 1995, 2004), random amplified polymorphic DNA (Wakui et al, 2013) and anonymous single nucleotide polymorphisms from genotyping‐by‐sequencing (Hirota et al, 2021; Murakami et al, 2020). These molecular phylogenetic studies showed that some intraspecific clades are weakly associated with geography.…”

Section: Introductionmentioning

confidence: 99%

Rear‐edge daylily populations show legacies of habitat fragmentation due to the Holocene climate warming

Masuda

Setoguchi

Nagasawa

et al. 2022

Journal of Biogeography

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Aims: Quaternary climate changes dramatically affected species' distributions and thus impacted genetic diversity patterns, particularly for rear-edge populations.Empirical studies have shown the southernmost (rear-edge), fragmented populations of Japanese woody plants can harbour high genetic diversity owing to their origin in southern glacial refugia. The effect of Holocene climate warming on rear-edge populations has, however, rarely been demonstrated. We assessed whether the genetic structure of populations of temperate plants in Japan can be interpreted to show legacies of both icy (Last Glacial Maximum, LGM) and warm (Holocene) climates.Location: Japanese Archipelago. Taxon: Hemerocallis middendorffii (Asphodelaceae).Methods: Population genetic profiles of 737 individuals from 41 populations were analysed to examine population structure and past population demography, using 12 EST-SSR markers. Present and past suitable habitat areas during the LGM and the Holocene climatic optimum were estimated by ecological niche modelling (ENM).Reconstructed palaeodistribution was combined with population genetics to statistically predict population demographics in relation to past climate changes.Results: Genetic analysis of the 41 populations revealed 6 regional population groups.Four groups widely dominating the northern-central ranges harboured high genetic diversity, whereas genetic divergence within the groups was low. In contrast, the two groups at the southwestern edge were geographically and genetically isolated, and they showed the lowest genetic diversity. The estimated palaeodistributions showed a decrease in the suitable range during the Holocene in comparison with that at the LGM, and only habitat suitability in the Holocene was able to predict the genetic diversity across the range. Main conclusions:Populations at the centre of the current distribution harbour high genetic diversity because they remained stable during both cold and warm periods.However, habitat fragmentation and population decline in relation to climate warming during the Holocene resulted in genetic isolation and impoverishment of the rearedge populations.

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“…Rhizomatous perennial. Flowers opening diurnal half-day, due to specialisation to diurnal moths ( Hirota et al 2021 ). Easily propagated by rhizomes, resulting in monoclonal cultivation ( Stout 1921 ).…”

Section: Taxon Treatmentsmentioning

confidence: 99%

The first checklist of alien vascular plants of Kyrgyzstan, with new records and critical evaluation of earlier data. Contribution 2

Sennikov¹,

Lazkov²

2022

BDJ

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We continue the inventory of alien vascular plants of Kyrgyzstan, with emphasis on the time and pathways of introduction of the species and their current status in the territory. Each taxon is discussed in the context of plant invasions in Central Asia. This work is a further development of the preliminary checklist of alien plants of Kyrgyzstan, which was compiled for the Global Register of Introduced and Invasive Species in 2018. This contribution includes all alien species of Kyrgyzstan belonging to Solanaceae and Asphodelaceae and one species of Asteraceae. Physalis philadelphicus (syn. P. ixocarpa) is reported for the first time from Central Asia, as new to Kazakhstan, Kyrgyzstan and Uzbekistan, thus marking a recent invasion with a variety of imported grain and seed material. The old records of P. ixocarpa from Uzbekistan are based on misidentified specimens of P. angulata. Physalis angulata is an old cotton immigrant in Central Asia, whose invasion started in the 1920s; it is excluded from the alien flora of Kyrgyzstan as registered in error on the basis of cultivated plants. Alkekengi officinarum is an archaeophyte of the Neolithic period in Central Asia, formerly used for food, now strongly declining and largely casual in Kyrgyzstan. The only historical record of Physalis viscosa from Uzbekistan was based on a technical error and belongs to A. officinarum. Datura stramonium and Hyoscyamus niger were introduced as medicinal plants during the period of the Arabic invasion of Central Asia, by the 11th century. Datura innoxia is a newly recorded casual alien, recently escaped from ornamental cultivation. Nicandra physalodes is a casual alien, which was cultivated by Russian colonists in the early 20th century for culinary use and is currently used in ornamental cultivation. Hemerocallis fulva was a remnant of historical cultivation in the former Khanate of Buxoro, and its formerly established colonies are presumably extinct in the wild. Bidens frondosa was seemingly introduced with contaminated forage and seed of American origin during the late Soviet period and started to spread in the period of independence; its invasion in the former USSR is analysed.

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Evolutionary history of Hemerocallis in Japan inferred from chloroplast and nuclear phylogenies and levels of interspecific gene flow

Cited by 17 publications

References 79 publications

Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping

Rear‐edge daylily populations show legacies of habitat fragmentation due to the Holocene climate warming

The first checklist of alien vascular plants of Kyrgyzstan, with new records and critical evaluation of earlier data. Contribution 2

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