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Article: Museum specimens: An overlooked and valuable material for conservation genetics

Nakahama, Naoyuki

Ecological research. 2021 Jan., v. 36, no. 1

2021

Abstract: Museum specimens include genetic information from when they were collected. This historical information, which is very difficult to ascertain from samples collected currently, could be a valuable material for use in conservation genetics. However, the ... ...

Abstract	Museum specimens include genetic information from when they were collected. This historical information, which is very difficult to ascertain from samples collected currently, could be a valuable material for use in conservation genetics. However, the genetic analysis of museum specimens is technically difficult because of DNA fragmentation and the deamination of cytosine to uracil. In recent years, various methods have been developed for the genetic analysis of museum specimens, such as data analysis techniques including next‐generation sequencing. The development of approaches that extract historical genetic information from museum specimens is expected to provide a new perspective on conservation genetics. This review focuses on the availability of museum specimens as genetic resources for conservation genetics. Some case studies are introduced, and perspectives on the future utility of conservation genetic studies using museum specimens are discussed. Moreover, recommended genetic analysis methods and important points for the usage of museum specimens are presented. This review provides a strong case for increasing the usage of museum specimens in conservation genetics studies in the future.
Keywords	DNA fragmentation ; conservation genetics ; cytosine ; deamination ; genetic analysis ; museums ; research ; uracil
Language	English
Dates of publication	2021-01
Size	p. 13-23.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	233459-8
ISSN	1440-1703 ; 0912-3814
ISSN (online)	1440-1703
ISSN	0912-3814
DOI	10.1111/1440-1703.12181
Database	NAL-Catalogue (AGRICOLA)

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Article: Habitat diversification associated with urban development has a little effect on genetic structure in the annual native plant

Taichi, Nakata / Nakahama, Naoyuki / Ohmido, Nobuko / Ushimaru, Atushi

Ecology and evolution

2024 Volume 14, Issue 2, Page(s) e10975

Abstract: Urban development greatly alters the natural and semi-natural habitats of native plants. Urbanisation results in a range of diverse habitats including remnant agricultural lands, urban parks, and roadside habitats. This habitat diversity often promotes ... ...

Abstract	Urban development greatly alters the natural and semi-natural habitats of native plants. Urbanisation results in a range of diverse habitats including remnant agricultural lands, urban parks, and roadside habitats. This habitat diversity often promotes trait divergence within urban areas. However, the mechanisms by which diverse urban habitats influence the population genetic structure of individual plant species remain poorly understood. We investigated the effects of urbanisation on genetic diversity and structure within 24
Language	English
Publishing date	2024-02-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.10975
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Integrative approach clarifies the distinct taxonomic account of gryloblattids endemic to Hokkaido, Japan, with a description of two new species (Insecta, Grylloblattodea)

Nakahama, Naoyuki / Yamasaki, Takeshi / Komazawa, Masaki / Nakano, Takafumi

Zoologischer Anzeiger. 2023 Jan., v. 302 p.17-27

2023

Abstract: Galloisiana yezoensis Asahina, 1961 was described on the basis of female specimens from the Ishikari Mountains, Hokkaido, Japan, and has been known as the only species of Grylloblattidae in Hokkaido. In preliminary research, several species closely ... ...

Abstract	Galloisiana yezoensis Asahina, 1961 was described on the basis of female specimens from the Ishikari Mountains, Hokkaido, Japan, and has been known as the only species of Grylloblattidae in Hokkaido. In preliminary research, several species closely related to G. yezoensis were collected from various sites in Hokkaido. In the present study, the taxonomic status of G. yezoensis and its relatives was reexamined through molecular and morphological analyses approaches. As a result, the phylogenetic tree of the COII region, and mitochondrial DNA, suggest that G. yezoensis and its relatives form a unique clade distinct from the Galloisiana clade. We therefore establish a new genus, Arctigalloisianagen. nov., with two new species, A. poropnetopasp. nov. and A. yubariensissp. nov. The type species is Arctigalloisiana yezoensiscomb. nov., and its male is described here for the first time.
Keywords	Grylloblattidae ; Japan ; females ; males ; mitochondrial DNA ; new genus ; new species ; phylogeny ; Arctigalloisiana ; Ice crawlers ; Morphological observation
Language	English
Dates of publication	2023-01
Size	p. 17-27.
Publishing place	Elsevier GmbH
Document type	Article ; Online
ZDB-ID	398-0
ISSN	1873-2674 ; 0044-5231
ISSN (online)	1873-2674
ISSN	0044-5231
DOI	10.1016/j.jcz.2022.11.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Contribution of genetic analyses to semi‐natural grassland biodiversity conservation in Japan

Nakahama, Naoyuki / Kurata, Seikan / Ushimaru, Atushi

Plant Species Biology. 2023 July, v. 38, no. 4 p.158-170

2023

Abstract: Semi‐natural grasslands maintained by moderate anthropogenic disturbance have been rapidly declining worldwide in recent decades, resulting in the progressive degradation of biodiversity therein. Similarly, in Japan, many semi‐natural grassland organisms ...

Abstract	Semi‐natural grasslands maintained by moderate anthropogenic disturbance have been rapidly declining worldwide in recent decades, resulting in the progressive degradation of biodiversity therein. Similarly, in Japan, many semi‐natural grassland organisms are threatened with extinction owing to the decline of semi‐natural grasslands, and their conservation and management has attracted considerable attention. Although ecological studies using genetic information are expected to contribute to the conservation of semi‐natural grassland organisms, no reviews have been conducted on the potential roles of these studies in grassland conservation in Japan. Here, we review the current trends in conservation‐ecological study on Japanese semi‐natural grassland organisms using genetic information by grouping into five categories: (1) monitoring of genetic diversity and spatial genetic structure, (2) exploration of the genetic consequences of management practices, (3) prevention of genetic disturbance, (4) elucidation of natural history traits, and (5) estimation of the origin and demography. Furthermore, the applicability of studies using high‐throughput sequencing, which has been rapidly progressing in recent years, is highlighted. This review provides the methods and perspectives on the use of genetic information to conserve biodiversity in semi‐natural grasslands.
Keywords	Japan ; anthropogenic activities ; biodiversity ; biodiversity conservation ; demography ; extinction ; genetic structure ; genetic variation ; grasslands ; natural history
Language	English
Dates of publication	2023-07
Size	p. 158-170.
Publishing place	John Wiley & Sons Australia, Ltd
Document type	Article ; Online
Note	REVIEW
ZDB-ID	2020484-X
ISSN	1442-1984 ; 0913-557X
ISSN (online)	1442-1984
ISSN	0913-557X
DOI	10.1111/1442-1984.12424
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Management and landscape of shelterbelts contribute to butterfly and flowering plant diversity in northern Japan

Nakahama, Naoyuki / Hayamizu, Masato / Iwasaki, Kenta / Nitta, Noritoshi

Ecological Research. 2022 Nov., v. 37, no. 6 p.780-790

2022

Abstract: A considerably large number of shelterbelts were established in Japan to increase crop yields in agricultural landscapes. Shelterbelt landscapes have multiple functions; they not only help to control wind damage but also to conserve biodiversity, ... ...

Abstract	A considerably large number of shelterbelts were established in Japan to increase crop yields in agricultural landscapes. Shelterbelt landscapes have multiple functions; they not only help to control wind damage but also to conserve biodiversity, including forest and grassland species. However, previous studies on biodiversity conservation in shelterbelts, and the target taxa were limited since this aspect of shelterbelts has not received much attention in Japan. This study examines the effects of shelterbelts and their regeneration on the diversity of butterflies and flowering plants in the Tokachi region of Hokkaido, Japan. Using a transect method, we compared environmental factors, butterfly, and flowering plant diversity in four habitats: inside forest, forest edge, regeneration sites, and semi‐natural grasslands which include shelterbelts and surrounding landscapes. There were significant differences in photosynthetically active radiation (PAR) among habitats, with higher PAR corresponding to higher numbers of butterfly species and individuals, and flowering plant species and flowers. Nonmetric multidimensional scaling results also showed that the species composition of flowering plants and butterflies differed among habitats. In addition, indicator value analysis showed that semi‐natural grasslands and regeneration sites were characterized by endangered butterflies and their host plants. Our results indicated that shelterbelt regeneration and the surrounding environment (e.g., semi‐natural grasslands) contributed to the diversity of butterflies and flowering plants, including endangered species. Future studies evaluating the diversity of various taxa would provide a more comprehensive understanding of the effects of shelterbelts on biodiversity conservation.
Keywords	Japan ; biodiversity conservation ; butterflies ; edge effects ; endangered species ; forests ; grasslands ; landscapes ; photosynthetically active radiation ; research ; shelterbelts ; species diversity ; wind damage
Language	English
Dates of publication	2022-11
Size	p. 780-790.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	233459-8
ISSN	1440-1703 ; 0912-3814
ISSN (online)	1440-1703
ISSN	0912-3814
DOI	10.1111/1440-1703.12342
Database	NAL-Catalogue (AGRICOLA)

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Article: A New Species of the Genus

Tomikawa, Ko / Nishimoto, Yuichiro / Nakahama, Naoyuki / Nakano, Takafumi

Zoological science

2022 Volume 39, Issue 5, Page(s) 489–499

Abstract: The subterranean amphipod ... ...

Abstract	The subterranean amphipod genus
MeSH term(s)	Amphipoda/genetics ; Animals ; Asia ; Far East ; Islands ; Japan ; Phylogeny
Language	English
Publishing date	2022-11-01
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2038883-4
ISSN	2212-3830 ; 0289-0003
ISSN (online)	2212-3830
ISSN	0289-0003
DOI	10.2108/zs220030
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The second phantom aquatic leaf beetle in Japan: Macroplea mutica rediscovery in the wetlands (Coleoptera: Chrysomelidae)

Nakahama, Naoyuki / Okano, Ryosuke / Nishimoto, Yuichiro / Nakatani, Yusuke / Noishiki, Asato / Ogawa, Naoki

Entomological Science. 2023 June, v. 26, no. 2 p.e12545-

2023

Abstract: Wetland biodiversity is currently declining on a global scale. Wetland biodiversity understanding is critical for determining the wetlands' conservation value. In this study, Macroplea Samouelle, 1819 (Coleoptera: Chrysomelidae) was discovered in Aomori ... ...

Abstract	Wetland biodiversity is currently declining on a global scale. Wetland biodiversity understanding is critical for determining the wetlands' conservation value. In this study, Macroplea Samouelle, 1819 (Coleoptera: Chrysomelidae) was discovered in Aomori Prefecture, Honshu Island, Japan. Only two Macroplea species have been recorded in Japan, M. japana (Jacoby, 1885) and M. mutica (Fabricius, 1792). Macroplea japana had been unrecorded for 60 years before being rediscovered in Honshu Island in 2022, and a single adult M. mutica female was discovered in Hokkaido Prefecture in 2003. The discovered individuals were concluded to be M. mutica based on morphological and molecular analyses. Although morphological differences were observed with the Eurasian M. mutica individuals, the male genitalia was nearly identical to M. mutica. For the molecular phylogenetic analysis based on COI and 28S sequences, Macroplea individuals in Japan were clustered with M. mutica on the Eurasian Continent. This is the first record of this species on Honshu Island (and the second in Japan), as well as the first record of adult males. This species would require conservation policies and additional distributional surveys.
Keywords	Chrysomelidae ; Japan ; adults ; biodiversity ; females ; male genitalia ; phylogeny ; wetlands
Language	English
Dates of publication	2023-06
Publishing place	John Wiley & Sons Australia, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2105599-3
ISSN	1479-8298 ; 1343-8786
ISSN (online)	1479-8298
ISSN	1343-8786
DOI	10.1111/ens.12545
Database	NAL-Catalogue (AGRICOLA)

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Article: Mitochondrial genetic structure reflects the geographical variation of elytral polymorphism frequency in Cheilomenes sexmaculata (Coleoptera: Coccinellidae)

Kawakami, Yasuko / Yamazaki, Kazuo / Ohashi, Kazunori / Nakahama, Naoyuki

Journal of Asia-Pacific entomology. 2021 Dec., v. 24, no. 4

2021

Abstract: Many ladybird species are known to have an elytral colour polymorphism, which indicates geographical variation. The ladybird beetle Cheilomenes sexmaculata (Fabricius) exhibits elytral colour polymorphism and has expanded its distribution from 33°N to 36° ...

Abstract	Many ladybird species are known to have an elytral colour polymorphism, which indicates geographical variation. The ladybird beetle Cheilomenes sexmaculata (Fabricius) exhibits elytral colour polymorphism and has expanded its distribution from 33°N to 36°N in Japan over 100 years since 1900. The mitochondrial COI gene haplotypes were integrated into two haplotype groups, with one group existing at higher frequencies in lower latitudes, the other group appearing at higher frequencies in higher latitudes. In addition, the dark morph types of this species increase with latitude, whereas the light types appear at higher relative frequencies in lower latitudes.In the present study, we first determined the morph types of individuals and examined the mitochondrial DNA COI gene. Second, we investigated the relationship between the genetic population structure based on the mitochondrial DNA COI gene and the morph types’ geographical variation. Results indicated that the mtCOI genetic structure was associated with the morph types by latitude; specifically, the haplotype group existing at higher frequencies in lower latitudes tended to be light morph types. In contrast, the haplotype dominant in higher latitudes more frequently exhibited dark morph types, indicating that dark morph types in the higher latitude genetic group may have led the distributional expansion toward higher latitudes since 1900 rather than the lower latitude light morph types.
Keywords	Cheilomenes ; Japan ; color ; entomology ; genes ; geographical variation ; haplotypes ; latitude ; mitochondria ; mitochondrial DNA ; population structure
Language	English
Dates of publication	2021-12
Size	p. 1270-1274.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1226-8615
DOI	10.1016/j.aspen.2021.08.016
Database	NAL-Catalogue (AGRICOLA)

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Article: Infestation of Phalaenopsis aphrodite Rchb.f. (Asparagales: Orchidaceae) flower buds by Japanagromyza tokunagai (Sasakawa) (Diptera: Agromyzidae) in a greenhouse on Shikoku Island, Japan

Suetsugu, Kenji / Nakahama, Naoyuki

Korean Society of Applied Entomology Journal of Asia-Pacific entomology. 2019 Sept., v. 22, no. 3

2019

Abstract: To protect endangered and commercially important orchid species, it is important to monitor and accurately identify orchid pests. Japanagromyza tokunagai (Sasakawa) larvae are known to infest the flower buds, stems, and ovaries of various Japanese orchid ...

Abstract	To protect endangered and commercially important orchid species, it is important to monitor and accurately identify orchid pests. Japanagromyza tokunagai (Sasakawa) larvae are known to infest the flower buds, stems, and ovaries of various Japanese orchid species. Given that J. tokunagai can infest diverse orchid hosts, J. tokunagai has the potential to be an economically important orchid pest in greenhouses. However, damage by J. tokunagai has previously only been reported in outdoor habitats. Here we revealed that the dipteran larvae infesting the flower buds of Phalaenopsis aphrodite Rchb.f. (Orchidaceae) cultivated in a greenhouse are J. tokunagai based on DNA barcoding, using COI sequences. Infested flower buds remained closed and eventually dropped to the ground, making the P. aphrodite plants commercially worthless. Phalaenopsis aphrodite is one of the most economically important ornamental orchids. Therefore, J. tokunagai is a potential threat to orchid production and we recommend taking precautions to prevent its spread.
Keywords	Agromyzidae ; DNA barcoding ; Phalaenopsis ; flower buds ; greenhouses ; habitats ; hosts ; insect larvae ; pests ; plant ovary ; stems ; Japan
Language	English
Dates of publication	2019-09
Size	p. 816-819.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1226-8615
DOI	10.1016/j.aspen.2019.06.014
Database	NAL-Catalogue (AGRICOLA)

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Article: Genetic structure, diversity and demography based on mitochondrial DNA analysis of Cheilomenes sexmaculata (Coleoptera: Coccinellidae)

Kawakami, Yasuko / Yamazaki, Kazuo / Ohashi, Kazunori / Nakahama, Naoyuki

Entomological science. 2020 Dec., v. 23, no. 4

2020

Abstract: Cheilomenes sexmaculata (Coleoptera: Coccinellidae) is widely distributed from intermediate latitude to equatorial regions. Here, we examined its genetic structure and diversity based on a 627 bp region of the mitochondrial COI gene. We then estimated ... ...

Abstract	Cheilomenes sexmaculata (Coleoptera: Coccinellidae) is widely distributed from intermediate latitude to equatorial regions. Here, we examined its genetic structure and diversity based on a 627 bp region of the mitochondrial COI gene. We then estimated its demographic changes over the past 30 000 years. We observed 22 haplotypes in 339 individuals from 29 sites in Japan and Taiwan. The 22 haplotypes were integrated into two haplotype groups: one group exists at higher frequencies in lower latitudes (22–26°N), whereas the other group appears at higher frequencies in higher latitudes (30–37°N). The effective population size of the group that predominates in higher latitudes increased from 15 000 to 10 000 years before present. In contrast, the size of the lower‐latitude group has remained constant for 30 000 years. These data suggest that C. sexmaculata might have expanded its distribution northwards and could be increasing its population size since the last glacial period.
Keywords	Cheilomenes ; Japan ; demography ; effective population size ; genes ; haplotypes ; latitude ; mitochondria ; mitochondrial DNA ; Taiwan
Language	English
Dates of publication	2020-12
Size	p. 385-392.
Publishing place	John Wiley & Sons Australia, Ltd
Document type	Article
Note	NAL-light ; JOURNAL ARTICLE
ZDB-ID	2105599-3
ISSN	1479-8298 ; 1343-8786
ISSN (online)	1479-8298
ISSN	1343-8786
DOI	10.1111/ens.12440
Database	NAL-Catalogue (AGRICOLA)

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