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Rainey TA, Tryc EE, Nicholson KE. Comparing skin swabs, buccal swabs, and toe clips for amphibian genetic sampling, a case study with a small anuran ( Acris blanchardi). Biol Methods Protoc 2024; 9:bpae030. [PMID: 38818027 PMCID: PMC11139508 DOI: 10.1093/biomethods/bpae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
Multiple methods for collecting genetic samples from amphibians exist, each with their own implications for study design, animal welfare, and costs. Toe clipping is one common method, but there is ongoing debate regarding its potential detriment. Less invasive methods should be implemented, if efficacious, as amphibians are a particularly vulnerable vertebrate group. Skin and buccal swabbing are less invasive methods for genetic sampling, but the potential for contamination and a lower yield of DNA may exist. To compare these methods, we gathered skin swabs, buccal swabs, and toe clips from the same individuals of a relatively small anuran species, Blanchard's Cricket Frog (Acris blanchardi). We then compared DNA yield, DNA purity, amplification success rate, and genotypic data quality among sample types. We found toe clips and buccal swabs generated similar DNA yield and purity, with skin swabs yielding significantly less DNA of significantly lower purity than the other sample types. Amplification success rate was significantly higher using toe clips compared to the other sample types, though buccal swab samples amplified more readily than skin swabs. Genotypic data from toe clips and buccal swabs did not differ significantly in quality, but skin swab data quality was significantly lowest among sample types. Thus, skin swabbing could produce erroneous data in some situations, but buccal swabbing is likely an effective substitute to toe clipping, even for small species. Our results can help future researchers select which genetic sampling method might best suit their research needs.
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Affiliation(s)
- Travis A Rainey
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Emily E Tryc
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
| | - Kirsten E Nicholson
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, United States
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Yoo N, Yoon JD, Yoo J, Kim KY, Heo JS, Kim KS. Development of molecular identification methods for Dryophytes suweonensis and D. japonicus, and their hybrids. PeerJ 2024; 12:e16728. [PMID: 38259669 PMCID: PMC10802155 DOI: 10.7717/peerj.16728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background As hybridization can reduce biodiversity or cause extinction, it is important to identify both purebred parental species and their hybrids prior to conserving them. The Suwon tree frog, Dryophytes suweonensis, is an endangered wildlife species in Korea that shares its habitat and often hybridizes with the Japanese tree frog, D. japonicus. In particular, D. suweonensis, D. japonicus, and their hybrids often have abnormal ovaries and gonads, which are known causes that could threaten their existence. Methods We collected 57 individuals from six localities where D. suweonensis is known to be present. High-resolution melting curve (HRM) analysis of the mitochondrial 12S ribosomal RNA gene was performed to determine the maternal species. Thereafter, the DNA sequences of five nuclear genes (SIAH, TYR, POMC, RAG1, and C-MYC) were analyzed to determine their parental species and hybrid status. Results The HRM analysis showed that the melting temperature of D. suweonensis was in the range of 79.0-79.3 °C, and that of D. japonicus was 77.7-78.0 °C, which clearly distinguished the two tree frog species. DNA sequencing of the five nuclear genes revealed 37 single-nucleotide polymorphism (SNP) sites, and STRUCTURE analysis showed a two-group structure as the most likely grouping solution. No heterozygous position in the purebred parental sequences with Q values ≥ 0.995 were found, which clearly distinguished the two treefrog species from their hybrids; 11 individuals were found to be D. suweonensis, eight were found to be D. japonicus, and the remaining 38 individuals were found to be hybrids. Conclusion Thus, it was possible to unambiguously identify the parental species and their hybrids using HRM analysis and DNA sequencing methods. This study provided fundamental information for D. suweonensis conservation and restoration research.
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Affiliation(s)
- Nakyung Yoo
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| | - Ju-Duk Yoon
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| | - Jeongwoo Yoo
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
| | - Keun-Yong Kim
- Department of Genetic Analysis, AquaGenTech Co., Ltd, Busan, Republic of Korea
| | - Jung Soo Heo
- Department of Genetic Analysis, AquaGenTech Co., Ltd, Busan, Republic of Korea
| | - Keun-Sik Kim
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang, Republic of Korea
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Andersen D, Maslova I, Purevdorj Z, Li JT, Messenger KR, Ren JL, Jang Y, Borzée A. East palearctic treefrog past and present habitat suitability using ecological niche models. PeerJ 2022; 10:e12999. [PMID: 35261821 PMCID: PMC8898549 DOI: 10.7717/peerj.12999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/02/2022] [Indexed: 01/11/2023] Open
Abstract
Ecological niche modeling is a tool used to determine current potential species' distribution or habitat suitability models which can then be used to project suitable areas in time. Projections of suitability into past climates can identify locations of climate refugia, or areas with high climatic stability likely to contain the highest levels of genetic diversity and stable populations when climatic conditions are less suitable in other parts of the range. Modeling habitat suitability for closely related species in recent past can also reveal potential periods and regions of contact and possible admixture. In the east palearctic, there are five Dryophytes (Hylid treefrog) clades belonging to two groups: Dryophytes japonicus group: Clades A and B; and Dryophytes immaculatus group: Dryophytes immaculatus, Dryophytes flaviventris, and Dryophytes suweonensis. We used maximum entropy modeling to determine the suitable ranges of these five clades during the present and projected to the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. We also calculated climatic stability for each clade to identify possible areas of climate refugia. Our models indicated suitable range expansion during the LGM for four clades with the exclusion of D. immaculatus. High climatic stability in our models corresponded to areas with the highest numbers of recorded occurrences in the present. The models produced here can additionally serve as baselines for models of suitability under climate change scenarios and indicate species ecological requirements.
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Affiliation(s)
- Desiree Andersen
- Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea
| | - Irina Maslova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of Sciences, Vladivostock, Russian Federation
| | - Zoljargal Purevdorj
- Department of Biology, Scholl of Mathematic and Natural Science, Mongolian State University of Education, Ulaanbaatar, Mongolia,Department of Forest and Environmental Resources, Chungnam National University, Daejeon, Republic of Korea
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, People’s Republic of China
| | | | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, People’s Republic of China
| | - Yikweon Jang
- Department of Life Science and Division of EcoScience, Ewha Womans University, Seoul, Republic of Korea,Interdisciplinary Program of EcoCreative, Ewha Womans University, Seoul, Republic of Korea
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
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Borzée A, Litvinchuk SN, Ri K, Andersen D, Nam TY, Jon GH, Man HS, Choe JS, Kwon S, Othman SN, Messenger K, Bae Y, Shin Y, Kim A, Maslova I, Luedtke J, Hobin L, Moores N, Seliger B, Glenk F, Jang Y. Update on Distribution and Conservation Status of Amphibians in the Democratic People's Republic of Korea: Conclusions Based on Field Surveys, Environmental Modelling, Molecular Analyses and Call Properties. Animals (Basel) 2021; 11:2057. [PMID: 34359183 PMCID: PMC8300379 DOI: 10.3390/ani11072057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Determining the range, status, ecology and behaviour of species from areas where surveys and samplings are uncommon or difficult to conduct is a challenge, such as in the Democratic People's Republic of Korea (DPR Korea). Here, we used genetic samples, field surveys, call recordings, photographic identification and a literature review to estimate the presence, range and status of amphibians in the DPR Korea. From our combined results and based on the IUCN Red List categories and criteria, we were able to estimate the national threat levels for most species. Our results demonstrated the presence of 18 native species and the suspected presence of Karsenia koreana and two Onychodactylus species. We reported the first record for Rana uenoi in the vicinity of Pyongyang using molecular tools and similarly confirmed the presence of Dryophytes japonicus at the same location. Based on distribution and modelling, we can expect the contact zone between species within the Rana and Onychodactylus genera to be located along the Changbai Massif, a mountain range that marks a shift in ecoregions and acts as a barrier to dispersion. The species richness was higher in the lowlands and at lower latitudes, with such areas populated by up to 11 species, while more northern regions were characterised by species richness of about half of that value. The combination of ecological models and known threats resulted in the recommendation of ten species as threatened at the national level following the IUCN Red List categories and criteria. This high number of threatened species was anticipated based on the high threat level to amphibians in bordering nations and globally. While the ecology of species in the DPR Korea is still understudied, we argue that species relying on agricultural wetlands such as rice paddies are not under imminent threat due to the enduring presence of extensive agricultural landscapes with low rates of chemical use and mechanisation. The maintenance of such landscapes is a clear benefit to amphibian species, in contrast to more industrialised agricultural landscapes in neighbouring nations. In comparison, the status of species dependent on forested habitats is unclear and threat levels are likely to be higher because of deforestation, as in neighbouring nations.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
| | - Spartak N. Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 St. Petersburg, Russia;
- Department of Zoology and Physiology, Dagestan State University, Gadzhiyev str. 43-a, Makhachkala, 3367000 Dagestan, Russia
| | - Kyongsim Ri
- Department of International Economic Cooperation, Ministry of Land and Environment Protection, Pyongyang, Democratic People’s Republic of Korea
| | - Desiree Andersen
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Tu Yong Nam
- Institute of Zoology, State Academy of Science, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Gwang Hyok Jon
- Department of Ecology, State Academy of Science, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Ho Song Man
- Department of Ecology, Life Science College, Kim Il Sung University, Ryongnam-dong, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Jong Sik Choe
- Department of Ecology, Life Science College, Kim Il Sung University, Ryongnam-dong, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Sera Kwon
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Siti N. Othman
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Kevin Messenger
- Herpetology and Applied Conservation Lab, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China;
| | - Yoonhyuk Bae
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Yucheol Shin
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
| | - Ajoung Kim
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Irina Maslova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Jennifer Luedtke
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
- Re:wild, Austin, TX 78746, USA
| | - Louise Hobin
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
| | - Nial Moores
- Birds Korea, 101-1902, Hyundai I Park, Busan 48559, Korea;
| | | | - Felix Glenk
- Hanns Seidel Foundation, Seoul 04419, Korea; (B.S.); (F.G.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea;
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Coexistence of Three Divergent mtDNA Lineages in Northeast Asia Provides New Insights into Phylogeography of Goldfish ( Carssius auratus). Animals (Basel) 2020; 10:ani10101785. [PMID: 33019665 PMCID: PMC7650769 DOI: 10.3390/ani10101785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/12/2020] [Accepted: 09/19/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Goldfish (Carassius auratus) is a well-known fish as food and as a pet, which is also frequently used as experimental animal. A unique mtDNA sequence was detected in a sample from our experimental station, which motivated us to study genetic constitution of goldfish in Northeast Asia. Three divergent mtDNA lineages were confirmed to coexist in this region. Two of which corresponded to the known lineages (C2 and C6), which was consistent with the zoogeographical records that there were two sympatric subspecies in Amur river basin. However, the third one (lineage C7) was largely neglected in the previous studies. Our results suggested lineage C7 had a wide distribution from Central Asia to Northeast Asia. Abstract Goldfish (Carassius aurautus), which is a middle size cyprinid, widely distribute throughout Eurasia. Phylogeographic studies using mtDNA markers have revealed several divergent lineages within goldfish. In this study, mtDNA variations were determined to elucidate the phylogeographical pattern and genetic structure of goldfish in Northeast Asia. A total of 1054 individuals from Amur river basin were analyzed, which including five newly collected populations and four previously reported populations. Three distinct mtDNA lineages were identified in those samples, two of which corresponded to two known lineages C2 and C6, respectively. The third lineage referred to as C7, following six known lineages of goldfish in mainland Eurasia. AMOVA results suggested that most of the genetic variations were among lineages, rather than among populations or twice samplings. We noted that the control region (CR) and cytochrome b (cytb) sequences of lineage C7 have been reported in previous studies, respectively. However, the evolutionary position and distribution pattern of this lineage was not discussed in the context of the species. Our results showed that “odd” CR and “hidden” cytb sequences from Central Asia represent the same mtDNA lineage of goldfish. The known samples of C7 lineage were collected from Central Asia (Eastern Kazakhstan and Western Mongolia) to East Asia (Northeast China and Far East Russia), which suggested that it had a wider distribution, rather than limit in Central Asia.
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Recommendations for IUCN Red List Conservation Status of the “Dryophytes immaculatus Group” in North East Asia. DIVERSITY 2020. [DOI: 10.3390/d12090336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Threat assessment is important to prioritize species conservation projects and planning. The taxonomic resolution regarding the status of the “Dryophytes immaculatus group” and the description of a new species in the Republic of Korea resulted in a shift in ranges and population sizes. Thus, reviewing the IUCN Red List status of the three species from the group: D. immaculatus, D. suweonensis and D. flaviventris and recommending an update is needed. While the three species have similar ecological requirements and are distributed around the Yellow Sea, they are under contrasting anthropological pressure and threats. Here, based on the literature available, I have applied all IUCN Red List criterion and tested the fit of each species in each criteria to recommend listing under the appropriate threat level. This resulted in the recommendation of the following categories: Near Threatened for D. immaculatus, Endangered following the criteria C2a(i)b for D. suweonensis and Critically Endangered following the criteria E for D. flaviventris. All three species are declining, mostly because of landscape changes as a result of human activities, but the differences in range, population dynamics and already extirpated subpopulations result in different threat levels for each species. Dryophytes flaviventris is under the highest threat category mostly because of its limited range segregated into two subpopulations; and several known extirpated subpopulations. Immediate actions for the conservation of this species are required. Dryophytes suweonensis is present in both the Republic of Korea and the Democratic Republic of Korea (DPR Korea) and is under lower ecological pressure in DPR Korea. Dryophytes immaculatus is present in the People’s Republic of China, over a very large range despite a marked decline. I recommend joint efforts for the conservation of these species.
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