1
|
Fu S, Chen X, Wang K, Chen J, Zhou J, Yi W, Lyu M, Ye Z, Bu W. Shared phylogeographic patterns and environmental responses of co-distributed soybean pests: Insights from comparative phylogeographic studies of Riptortus pedestris and Riptortus linearis in the subtropics of East Asia. Mol Phylogenet Evol 2024; 195:108055. [PMID: 38485106 DOI: 10.1016/j.ympev.2024.108055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/31/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Comparative phylogeographic studies of closely related species sharing co-distribution areas can elucidate the role of shared historical factors and environmental changes in shaping their phylogeographic pattern. The bean bugs, Riptortus pedestris and Riptortus linearis, which both inhabit subtropical regions in East Asia, are recognized as highly destructive soybean pests. Many previous studies have investigated the biological characteristics, pheromones, chemicals and control mechanisms of these two pests, but few studies have explored their phylogeographic patterns and underlying factors. In this study, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) dataset to investigate phylogeographic patterns and construct ecological niche models (ENM) for both Riptortus species. Our findings revealed similar niche occupancies and population genetic structures between the two species, with each comprising two phylogeographic lineages (i.e., the mainland China and the Indochina Peninsula clades) that diverged approximately 0.1 and 0.3 million years ago, respectively. This divergence likely resulted from the combined effects of temperatures variation and geographical barriers in the mountainous regions of Southwest China. Further demographic history and ENM analyses suggested that both pests underwent rapid expansion prior to the Last Glacial Maximum (LGM). Furthermore, ENM predicts a northward shift of both pests into new soybean-producing regions due to global warming. Our study indicated that co-distribution soybean pests with overlapping ecological niches and similar life histories in subtropical regions of East Asia exhibit congruent phylogeographic and demographic patterns in response to shared historical biogeographic drivers.
Collapse
Affiliation(s)
- Siying Fu
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xin Chen
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China(2)
| | - Kaibin Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Juhong Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiayue Zhou
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wenbo Yi
- Department of Biology, Xinzhou Normal University, Xinzhou, Shanxi, China(2)
| | - Minhua Lyu
- Nanchang University, Affiliated Hospital 1, Jiangxi, China(2)
| | - Zhen Ye
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| |
Collapse
|
2
|
Qin SY, Zuo ZY, Xu SX, Liu J, Yang FM, Luo YH, Ye JW, Zhao Y, Rong J, Liu B, Ma PF, Li DZ. Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14180. [PMID: 37700668 DOI: 10.1111/cobi.14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/09/2023] [Accepted: 06/12/2023] [Indexed: 09/14/2023]
Abstract
Current biodiversity loss is generally considered to have been caused by anthropogenic disturbance, but it is unclear when anthropogenic activities began to affect biodiversity loss. One hypothesis suggests it began with the Industrial Revolution, whereas others propose that anthropogenic disturbance has been associated with biodiversity decline since the early Holocene. To test these hypotheses, we examined the unique vegetation of evergreen broadleaved forests (EBLFs) in East Asia, where humans have affected landscapes since the early Holocene. We adopted a genomic approach to infer the demographic history of a dominant tree (Litsea elongata) of EBLFs. We used Holocene temperature and anthropogenic disturbance factors to calculate the correlation between these variables and the historical effective population size of L. elongata with Spearman statistics and integrated the maximum-entropy niche model to determine the impact of climate change and anthropogenic disturbance on fluctuation in its effective population size. We identified 9 well-defined geographic clades for the populations of L. elongata. Based on the estimated historical population sizes of these clades, all the populations contracted, indicating persistent population decline over the last 11,000 years. Demographic history of L. elongata and human population change, change in cropland use, and change in irrigated rice area were significantly negatively correlated, whereas climate change in the Holocene was not correlated with demographic history. Our results support the early human impact hypothesis and provide comprehensive evidence that early anthropogenic disturbance may contribute to the current biodiversity crisis in East Asia.
Collapse
Affiliation(s)
- Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shuang-Xiu Xu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Feng-Mao Yang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Wei Ye
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
3
|
Han EK, Tamaki I, Oh SH, Park JS, Cho WB, Jin DP, Kim BY, Yang S, Son DC, Choi HJ, Gantsetseg A, Isagi Y, Lee JH. Genetic and demographic signatures accompanying the evolution of the selfing syndrome in Daphne kiusiana, an evergreen shrub. ANNALS OF BOTANY 2023; 131:751-767. [PMID: 36469429 PMCID: PMC10184445 DOI: 10.1093/aob/mcac142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/23/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The evolution of mating systems from outcrossing to self-fertilization is a common transition in flowering plants. This shift is often associated with the 'selfing syndrome', which is characterized by less visible flowers with functional changes to control outcrossing. In most cases, the evolutionary history and demographic dynamics underlying the evolution of the selfing syndrome remain poorly understood. METHODS Here, we characterize differences in the demographic genetic consequences and associated floral-specific traits between two distinct geographical groups of a wild shrub, Daphne kiusiana, endemic to East Asia; plants in the eastern region (southeastern Korea and Kyushu, Japan) exhibit smaller and fewer flowers compared to those of plants in the western region (southwestern Korea). Genetic analyses were conducted using nuclear microsatellites and chloroplast DNA (multiplexed phylogenetic marker sequencing) datasets. KEY RESULTS A high selfing rate with significantly increased homozygosity characterized the eastern lineage, associated with lower levels of visibility and herkogamy in the floral traits. The two lineages harboured independent phylogeographical histories. In contrast to the western lineage, the eastern lineage showed a gradual reduction in the effective population size with no signs of a severe bottleneck despite its extreme range contraction during the last glacial period. CONCLUSIONS Our results suggest that the selfing-associated morphological changes in D. kiusiana are of relatively old origin (at least 100 000 years ago) and were driven by directional selection for efficient self-pollination. We provide evidence that the evolution of the selfing syndrome in D. kiusiana is not strongly associated with a severe population bottleneck.
Collapse
Affiliation(s)
- Eun-Kyeong Han
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu 501-3714, Japan
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, Daejeon 34520, Republic of Korea
| | - Jong-Soo Park
- Department of Botany, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Won-Bum Cho
- Department of Plant Variety Protection, National Forest Seed and Variety Center, Chungju 27495, Republic of Korea
| | - Dong-Pil Jin
- Urban Biodiversity Research Division, Sejong National Arboretum, Sejong 30106, Republic of Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea
| | - Amarsanaa Gantsetseg
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| |
Collapse
|
4
|
Yoichi W, Tamaki I, Oh SH, Nagano AJ, Uehara K, Tomaru N, Abe H. The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment. AMERICAN JOURNAL OF BOTANY 2023; 110:e16166. [PMID: 37074769 DOI: 10.1002/ajb2.16166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 05/03/2023]
Abstract
PREMISE The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula. METHODS We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses. RESULTS The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance. CONCLUSIONS The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.
Collapse
Affiliation(s)
- Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, Japan
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, 62 Daehak-ro, Dong-gu, Daejeon, 34520, South Korea
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Koichi Uehara
- College of Liberal Arts and Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Harue Abe
- Sado Island Center for Ecological Sustainability, Niigata University, 94-2 Koda, Sado, Niigata, 952-2206, Japan
| |
Collapse
|
5
|
Lyu R, Xiao J, Li M, Luo Y, He J, Cheng J, Xie L. Phylogeny and Historical Biogeography of the East Asian Clematis Group, Sect. Tubulosae, Inferred from Phylogenomic Data. Int J Mol Sci 2023; 24:3056. [PMID: 36769378 PMCID: PMC9917980 DOI: 10.3390/ijms24033056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023] Open
Abstract
The evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, has not been comprehensively studied. In this study, we reconstruct the phylogeny of this section with a complete sampling using a phylogenomic approach. The genome skimming method was applied to obtain the complete plastome sequence, the nuclear ribosomal DNA (nrDNA), and the nuclear SNPs data for phylogenetic reconstruction. Using a Bayesian molecular clock approach and ancestral range reconstruction, we reconstruct biogeographical history and discuss the biotic and abiotic factors that may have shaped the distribution patterns of the section. Both nuclear datasets better resolved the phylogeny of the sect. Tubulosae than the plastome sequence. Sect. Tubulosae was resolved as a monophyletic group sister to a clade mainly containing species from the sect. Clematis and sect. Aspidanthera. Within sect. Tubulosae, two major clades were resolved by both nuclear datasets. Two continental taxa, C. heracleifolia and C. tubulosa var. ichangensis, formed one clade. One continental taxon, C. tubulosa, and all the other species from Taiwan island, the Korean peninsula, and the Japanese archipelago formed the other clade. Molecular dating results showed that sect. Tubulosae diverged from its sister clade in the Pliocene, and all the current species diversified during the Pleistocene. Our biogeographical reconstruction suggested that sect. Tubulosae evolved and began species diversification, most likely in mainland China, then dispersed to the Korean peninsula, and then expanded its range through the Japanese archipelago to Taiwan island. Island species diversity may arise through allopatric speciation by vicariance events following the range fragmentation triggered by the climatic oscillation and sea level change during the Pleistocene epoch. Our results highlight the importance of climatic oscillation during the Pleistocene to the spatial-temporal diversification patterns of the sect. Tubulosae.
Collapse
Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Mingyang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| |
Collapse
|
6
|
Zhang T, Meng J, Yang F, Li X, Yin X, Zhang J, He S. Genome-wide assessment of population genetic and demographic history in Magnolia odoratissima based on SLAF-seq. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01500-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
7
|
Chimura K, Akita S, Iwasaki T, Nagano AJ, Shimada S. Phylogeography of a canopy-forming kelp, Eisenia bicyclis (Laminariales, Phaeophyceae), based on a genome-wide sequencing analysis. JOURNAL OF PHYCOLOGY 2022; 58:318-329. [PMID: 35000198 DOI: 10.1111/jpy.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Analyses of phylogeographic patterns and genetic diversity provide fundamental information for the management and conservation of species. However, little is published about these patterns in Japanese kelp species. In this study, we conducted phylogeographic analyses of a canopy-forming kelp, Eisenia bicyclis, based on genome-wide SNPs identified by ddRAD-seq. We obtained 1,299 SNPs for 76 samples from nine localities across the distribution. STRUCTURE, NeighborNet, and discriminant analysis of principal components consistently showed high genetic differentiation among the Eastern Pacific, Central Pacific, and Sea of Japan coastal regions. Relatively strong gene flow was detected only within populations in the Eastern Pacific and in the Sea of Japan. Genetic diversity and genetic uniqueness were high in the Central Pacific and low in the Sea of Japan. These results suggest that there were at least three independent refugia corresponding to the three regions during the Last Glacial Maximum (LGM). Furthermore, relatively larger populations in the Central Pacific and smaller populations in the Sea of Japan have been maintained in the demographic history from before the LGM to the present. These phylogeographic histories were supported by an Approximate Bayesian Computation analysis. From a conservation genetics perspective, the loss of southern populations in the Central Pacific would greatly reduce the total genetic diversity of the species. Southern populations in the Sea of Japan, which have relatively low genetic diversity, may be highly vulnerable to environmental change, such as heat waves and increased feeding. Therefore, careful monitoring and conservation are needed in the two regions.
Collapse
Affiliation(s)
- Kanako Chimura
- Humanities and Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
| | - Shingo Akita
- Natural Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
- Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido, 041-8611, Japan
| | - Takaya Iwasaki
- Natural Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Satoshi Shimada
- Natural Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
| |
Collapse
|
8
|
Li J, Cai J, Qin HH, Price M, Zhang Z, Yu Y, Xie DF, He XJ, Zhou SD, Gao XF. Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 12:699226. [PMID: 35178055 PMCID: PMC8845482 DOI: 10.3389/fpls.2021.699226] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Tribe Lilieae, encompassing Lilium, Notholirion, Cardiocrinum, and Fritillaria, includes economically important crops with a horticultural and medicinal value. It is considered to be a core lineage of Liliaceae, but phylogenetic relationships within it, and the timing of the origin of individual clades, remain incompletely resolved. To address these issues, we reconstructed the evolutionary history of the tribe. We sequenced 45 Liliaceae plastomes and combined them with publicly available data (for a total of 139 plastomes) to explore the systematics, origin, divergence, and evolution of Lilieae. Our taxon sampling covers all ten sections of Lilium, all Cardiocrinum species, three Notholirion species, and major phylogenetic clades of Fritillaria. Our phylogenetic analysis confirms the monophyly of major sections/subgenera of Lilium and Fritillaria with strong support. We dated the origin of Lilieae to the Eocene, with genera and species radiations inferred to have occurred in the Miocene. The reconstruction of the ancestral area implies that Lilieae may have originated from the Qinghai-Tibet Plateau (QTP): the Himalayas and Hengduan Mountains and uplifting of the QTP likely promoted divergence within the tribe. Ancestral-state reconstructions of the bulb component number (including bulblets and scales) show a strong correlation with the genus-level phylogenetic diversity in Lilieae. They also predict that the most recent common ancestor of Lilieae had bulbs with numerous bulblets. Based on these observations, we predicted that climatic oscillations associated with the QTP uplift played an important role in the evolution of the Lilieae bulb. Our findings provide a well-supported picture of evolutionary relationships and a useful framework for understanding the pathway of bulb evolution within Lilieae, contributing to a better understanding of the evolutionary history of lilies.
Collapse
Affiliation(s)
- Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|
9
|
Sata H, Shimizu M, Iwasaki T, Ikeda H, Soejima A, Kozhevnikov AE, Kozhevnikova ZV, Im HT, Jang SK, Azuma T, Nagano AJ, Fujii N. Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data. JOURNAL OF PLANT RESEARCH 2021; 134:1181-1198. [PMID: 34595677 DOI: 10.1007/s10265-01339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 05/23/2023]
Abstract
To elucidate the origin and migration history of the "Mansen elements," a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000 years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further post-glacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.
Collapse
Affiliation(s)
- Haruna Sata
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Midori Shimizu
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Takaya Iwasaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Akiko Soejima
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Andrey E Kozhevnikov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Zoya V Kozhevnikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Hyoung-Tak Im
- Department of Biological Science, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Kil Jang
- East Coast Research Institute of Life Science, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung city, Gangwon-do, 25457, South Korea
| | - Takayuki Azuma
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, N3W8, Chuo-ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Noriyuki Fujii
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
- Course of Biological Science, Faculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
| |
Collapse
|
10
|
Sata H, Shimizu M, Iwasaki T, Ikeda H, Soejima A, Kozhevnikov AE, Kozhevnikova ZV, Im HT, Jang SK, Azuma T, Nagano AJ, Fujii N. Phylogeography of the East Asian grassland plant, Viola orientalis (Violaceae), inferred from plastid and nuclear restriction site-associated DNA sequencing data. JOURNAL OF PLANT RESEARCH 2021; 134:1181-1198. [PMID: 34595677 DOI: 10.1007/s10265-021-01339-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
To elucidate the origin and migration history of the "Mansen elements," a group of temperate grassland plants mainly distributed in northeastern Asia, phylogeographic analyses based on chloroplast DNA markers and double-digest restriction site-associated DNA sequencing (ddRAD-seq) data were performed on Viola orientalis, one of the representative species of the group. Phylogenetic analyses using ddRAD-seq data revealed that the populations of V. orientalis were clustered into five clades, among which the continental clades made of populations from Russia and Korea diverged more than 100,000 years earlier than the Japanese clades. The Japanese clade likely diverged during the last glacial period, followed by a further post-glacial divergence into the Kyushu and the Honshu subclades. Our study demonstrated that V. orientalis originated in the continental area of northeastern Asia and, during the last glacial period, has spread southward through the Korean Peninsula across the Japanese Islands. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.
Collapse
Affiliation(s)
- Haruna Sata
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Midori Shimizu
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Takaya Iwasaki
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Akiko Soejima
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan
| | - Andrey E Kozhevnikov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Zoya V Kozhevnikova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Hyoung-Tak Im
- Department of Biological Science, Chonnam National University, Gwangju, 61186, South Korea
| | - Su-Kil Jang
- East Coast Research Institute of Life Science, Gangneung-Wonju National University, Jukheon-gil 7, Gangneung city, Gangwon-do, 25457, South Korea
| | - Takayuki Azuma
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, N3W8, Chuo-ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Noriyuki Fujii
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
- Course of Biological Science, Faculty of Science, Kumamoto University, 2-39-1 Kurokami, Chuo, Kumamoto, Kumamoto, 860-8555, Japan.
| |
Collapse
|
11
|
Yao H, Zhang Y, Wang Z, Liu G, Ran Q, Zhang Z, Guo K, Yang A, Wang N, Wang P. Inter-glacial isolation caused divergence of cold-adapted species: the case of the snow partridge. Curr Zool 2021; 68:489-498. [PMID: 36090147 PMCID: PMC9450178 DOI: 10.1093/cz/zoab075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Deciphering the role of climatic oscillations in species divergence helps us understand the mechanisms that shape global biodiversity. The cold-adapted species may have expanded their distribution with the development of glaciers during glacial period. With the retreat of glaciers, these species were discontinuously distributed in the high-altitude mountains and isolated by geographical barriers. However, the study that focuses on the speciation process of cold-adapted species is scant. To fill this gap, we combined population genetic data and ecological niche models (ENMs) to explore divergence process of snow partridge (Lerwa lerwa). Lerwa lerwa is a cold-adapted bird that is distributed from 4,000 to 5,500 m. We found 2 genetic populations within L. lerwa, and they diverged from each other at about 0.40–0.44 million years ago (inter-glacial period after Zhongliangan glaciation). The ENMs suggested that L. lerwa expanded to the low elevations of the Himalayas and Hengduan mountains during glacial period, whereas it contracted to the high elevations, southern of Himalayas, and Hengduan mountains during inter-glacial periods. Effective population size trajectory also suggested that L. lerwa expanded its population size during the glacial period. Consistent with our expectation, the results support that inter-glacial isolation contributed to the divergence of cold-adapted L. lerwa on Qinghai-Tibetan Plateau. This study deepens our understanding of how climatic oscillations have driven divergence process of cold-adapted Phasianidae species distributed on mountains.
Collapse
Affiliation(s)
- Hongyan Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Yanan Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Zhen Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Hangzhou Xi’ao Environmental Science Technique Company Limited, Zhejiang 310011, China
| | - Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Ran
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Yancheng Wetland and World Natural Heritage Conservation and Management Center, Jiangsu 224000, China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Keji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland Administration, Changsha 410014, China
| | - Ailin Yang
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Nan Wang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
12
|
Tamaki I, Obora T, Ohsawa T, Matsumoto A, Saito Y, Ide Y. Different population size change and migration histories created genetic diversity of three oaks in Tokai region, central Japan. JOURNAL OF PLANT RESEARCH 2021; 134:933-946. [PMID: 34155542 DOI: 10.1007/s10265-021-01323-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
To understand genetic diversity in focal species, it is important to consider the possibility of speciation with gene flow, especially in species with porous genomes such as oaks. We studied genetic diversity and structure in three oaks, Quercus mongolica var. mongolicoides (QM), Q. mongolica var. crispula (QC) and Q. serrata (QS), growing in the Tokai region, central Japan. QM is semi-endemic to the region while the others are common taxa. We also conducted demographic modeling to infer their population size change and migration histories using an approximate Bayesian computation (ABC) approach. The three taxa showed distinct genetic structures but there was genetic admixture among the taxa, especially between QM and QC. ABC analysis of population size change revealed that the population size of QM was stable during and after the last glacial period, while QC and QS showed population expansion after the last glacial maximum. ABC analysis of population divergence and migration revealed that continuous gene flow between QM and QC after their divergence was supported, while between QM and QS, and between QC and QS, secondary contact after sufficient isolation was supported. These historical migration patterns among the three taxa indicate that QM and QC are currently in the early stage or gray zone of speciation, whereas speciation of the other two taxon pairs is considered to have almost been established. Observed gene flow patterns and strength between QM and QC, and between QM and QS, were explained by both flowering patterns and historical distributions, but those between QC and QS were not.
Collapse
Affiliation(s)
- Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan.
| | - Tomohiro Obora
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, 501-3714, Japan
| | - Takafumi Ohsawa
- Ministry of the Environment, 1-2-2 Kasumigaseki, Chiyoda-ku, Tokyo, 100-8975, Japan
| | - Asako Matsumoto
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Yoko Saito
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuji Ide
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| |
Collapse
|
13
|
Xue C, Geng FD, Li JJ, Zhang DQ, Gao F, Huang L, Zhang XH, Kang JQ, Zhang JQ, Ren Y. Divergence in the Aquilegia ecalcarata complex is correlated with geography and climate oscillations: Evidence from plastid genome data. Mol Ecol 2021; 30:5796-5813. [PMID: 34448283 DOI: 10.1111/mec.16151] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/03/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
Quaternary climate oscillations and geographical heterogeneity play important roles in determining species and genetic diversity distribution patterns, but how these factors affect the migration and differentiation of East Asian plants species at the population level remains poorly understood. The Aquilegia ecalcarata complex, a group that originated in the Late Tertiary and is widely distributed throughout East Asia, displays high genetic variation that is suitable for studying elaborate phylogeographic patterns and demographic history related to the impact of Quaternary climate and geography. We used plastid genome data from 322 individuals in 60 populations of the A. ecalcarata complex to thoroughly explore the impact of Quaternary climate oscillations and geography on the phylogeographic patterns and demographic history of the A. ecalcarata complex through a series of phylogenetic, divergence time estimation, and demographic history analyses. The dry, cold climate and frequent climate oscillations that occurred during the early Pleistocene and the Mid-Pleistocene transition led to the differentiation of the A. ecalcarata complex, which was isolated in various areas. Geographically, the A. ecalcarata complex can be divided into Eastern and Western Clades and five subclades, which conform to the divergence of the East Asian flora. Our results clearly show the impact of Quaternary climate and geography on evolutionary history at the population level. These findings promote the understanding of the relationship between plant genetic differentiation and climate and geographical factors of East Asia at the population level.
Collapse
Affiliation(s)
- Cheng Xue
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Fang-Dong Geng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Jiao-Jie Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Dan-Qing Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Fei Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Xiao-Hui Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Ju-Qing Kang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| | - Yi Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Science, Shaanxi Normal University, Xi'an, China
| |
Collapse
|
14
|
Gai Z, Zhai J, Chen X, Jiao P, Zhang S, Sun J, Qin R, Liu H, Wu Z, Li Z. Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China. FRONTIERS IN PLANT SCIENCE 2021; 12:705083. [PMID: 34456946 PMCID: PMC8385373 DOI: 10.3389/fpls.2021.705083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/14/2021] [Indexed: 05/28/2023]
Abstract
Populus sect. Turanga (hereafter referred to as "Populus"), including Populus euphratica and Populus pruinosa, are the predominant tree species in desert riparian forests in northwestern China. These trees play key roles in maintaining ecosystem balance, curbing desertification, and protecting biodiversity. However, the distribution area of Populus forests has been severely diminished and degraded in recent years due to increased habitat destruction and human activity. Understanding the genetic diversity among Populus individuals and populations is essential for designing conservation strategies, but comprehensive studies of their genetic diversity in northwest China are lacking. Here, we assessed the population structures and genetic diversity of 1,620 samples from 85 natural populations of Populus (59 P. euphratica and 26 P. pruinosa populations) covering all of northwestern China using 120 single nucleotide polymorphism (SNP) markers. Analysis of population structure revealed significant differentiation between these two sister species and indicated that strong geographical distribution patterns, a geographical barrier, and environmental heterogeneity shaped the extant genetic patterns of Populus. Both P. euphratica and P. pruinosa populations in southern Xinjiang had higher genetic diversity than populations in other clades, perhaps contributing to local geographic structure and strong gene flow. Analysis of molecular variance (AMOVA) identified 15% variance among and 85% variance within subpopulations. Mantel tests suggested that the genetic variation among P. euphratica and P. pruinosa populations could be explained by both geographical and environmental distance. The genetic diversity of P. euphratica showed a significant negative correlation with latitude and longitude and a positive correlation with various environmental factors, such as precipitation of warmest quarter and driest month, temperature seasonality, and annual mean temperature. These findings provide insights into how the genetic differentiation of endangered Populus species was driven by geographical and environmental factors, which should be helpful for designing strategies to protect these genetic resources in the future.
Collapse
Affiliation(s)
- Zhongshuai Gai
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Juntuan Zhai
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Xiangxiang Chen
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Peipei Jiao
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Shanhe Zhang
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Jianhao Sun
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Zhijun Li
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin, Xinjiang Production and Construction Group, Alar, China
- College of Life Sciences, Tarim University, Alar, China
- Desert Poplar Research Center of Tarim University, Alar, China
| |
Collapse
|
15
|
Genetic Distinctiveness but Low Diversity Characterizes Rear-Edge Thuja standishii (Gordon) Carr. (Cupressaceae) Populations in Southwest Japan. DIVERSITY 2021. [DOI: 10.3390/d13050185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (Fst = 0.087), with northeast populations weakly differentiated (Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged (Fst = 0.168), but contained few unique alleles with lower genetic diversity (Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles.
Collapse
|
16
|
Sakaguchi S, Asaoka Y, Takahashi D, Isagi Y, Imai R, Nagano AJ, Qiu YX, Li P, Lu R, Setoguchi H. Inferring historical survivals of climate relicts: the effects of climate changes, geography, and population-specific factors on herbaceous hydrangeas. Heredity (Edinb) 2021; 126:615-629. [PMID: 33510468 PMCID: PMC8115046 DOI: 10.1038/s41437-020-00396-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/25/2020] [Accepted: 12/08/2020] [Indexed: 01/29/2023] Open
Abstract
Climate relicts hold considerable importance because they have resulted from numerous historical changes. However, there are major interspecific variations among the ways by which they survived climate changes. Therefore, investigating the factors and timing that affected population demographics can expand our understanding of how climate relicts responded to historical environmental changes. Here, we examined herbaceous hydrangeas of genus Deinanthe in East Asia, which show limited distributions and a remarkable disjunction between Japan and central China. Chloroplast genome and restriction site-associated DNA sequencing revealed that speciation event occurred in the late Miocene (ca. 7-9 Mya) in response to global climate change. Two lineages apparently remained not branched until the middle Quaternary, and afterwards started to diverge to regional population groups. The narrow endemic species in central China showed lower genetic diversity (He = 0.082), as its population size rapidly decreased during the Holocene due to isolation in montane refugia. Insular populations in the three Japanese islands (He = 0.137-0.160) showed a genetic structure that was inconsistent with sea barriers, indicating that it was shaped in the glacial period when its range retreated to coastal refugia on the exposed sea floor. Demographic modelling by stairway-plot analysis reconstructed variable responses of Japanese populations: some experienced glacial bottlenecks in refugial isolation, while post-glacial range expansion seemingly exerted founder effects on other populations. Overall, this study demonstrated the involvement of not just one, but multiple factors, such as the interplay between climate changes, geography, and other population-specific factors, that determine the demographics of climate relicts.
Collapse
Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan.
| | - Yui Asaoka
- Faculty of Integrated Human Studies, Kyoto University, Kyoto, 606-8501, Japan
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryosuke Imai
- Iriomote Station, Tropical Biosphere Research Centre, University of the Ryukyus, Okinawa, 907-1541, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
| | - Ying-Xiong Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ruisen Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, 606-8501, Japan
| |
Collapse
|
17
|
Ye Z, Chen D, Yuan J, Zheng C, Yang X, Wang W, Zhang Y, Wang S, Jiang K, Bu W. Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae). Mol Ecol 2020; 29:4573-4587. [PMID: 33006793 DOI: 10.1111/mec.15669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Genetic stochasticity and bottlenecking in the course of Pleistocene glaciations have been identified as threatening the survival of local endemics. However, the mechanisms by which local endemic species balance the influences of these two events remain poorly understood. Here, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) data set, mined mitochondrial sequences and constructed ecological niche models for the island endemic water strider Metrocoris esakii (Hemiptera: Gerridae). We found that M. esakii comprised three divergent lineages (i.e., north, central and south) isolated by geographical barriers and generally experienced population declines with the constriction of suitable areas during the Last Glacial Maximum (LGM). Further demographic model testing and stairway plots revealed a history of recent gene flow among the neighbouring lineages and rapid recovery at the end of the LGM, indicating that M. esakii at least had the potential for an adaptive response to population fragmentation and bottlenecking. The northern lineage did not show genetic bottlenecking during the LGM, which was probably due to its large effective population size (Ne ) from migration, which improved its adaptive potential. Relative to the ddRAD-seq data set, the demographic results based on mitochondrial sequences were less conclusive, showing weak differentiation and oversimplified demographic trajectories for the three genetic lineages. Overall, this study provides some degree of optimism for the survival of island endemic water striders from a demographic perspective, but further evaluation of their extinction risk under the impacts of human activities is required.
Collapse
Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Danyang Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Juanjuan Yuan
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xin Yang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenwu Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yaoyao Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Siqi Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
18
|
Feng Y, Comes HP, Qiu YX. Phylogenomic insights into the temporal-spatial divergence history, evolution of leaf habit and hybridization in Stachyurus (Stachyuraceae). Mol Phylogenet Evol 2020; 150:106878. [DOI: 10.1016/j.ympev.2020.106878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 05/07/2020] [Accepted: 06/01/2020] [Indexed: 12/14/2022]
|