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Ikeda H. Virtual issue: phylogeographic studies in the Japanese Archipelago: from geographic patterns of genetic variation to biodiversity in plants. JOURNAL OF PLANT RESEARCH 2023; 136:581-585. [PMID: 37462882 DOI: 10.1007/s10265-023-01478-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 08/12/2023]
Abstract
Phylogeographic studies have investigated genetic variation and structure within species or closely related lineages and are fundamental for understanding factors and processes of genetic divergence as well as speciation. This virtual issue collects 35 papers on phylogeographic studies published in the Journal of Plant Research and focuses on three major topics in biodiversity: (1) biogeography, (2) systematics, and (3) evolution.
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Affiliation(s)
- Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
- Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Tokyo, Meguro-ku, 153-8902, Japan.
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Kitamura K, Namikawa K, Tsuda Y, Kobayashi M, Matsui T. Possible northern persistence of Siebold's beech, Fagus crenata, at its northernmost distribution limit on an island in Japan Sea: Okushiri Island, Hokkaido. FRONTIERS IN PLANT SCIENCE 2022; 13:990927. [PMID: 36589061 PMCID: PMC9797532 DOI: 10.3389/fpls.2022.990927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Siebold's beech, Fagus crenata, is widely distributed across the Japanese Archipelago and islands in Japan Sea. Similar to the northern limit of the geographical distribution of F. crenata on the mainland of Hokkaido, the northern limit of the distribution of F. crenata on islands in the Japan Sea is observed on Okushiri Island (ca 42°N). To understand the genetic relationships of F. crenata on Okushiri Island, we examined chloroplast (cp) DNA haplotypes and 11 nuclear microsatellite (SSR) loci among 1,838 individuals from 44 populations from Okushiri Island, mainland Hokkaido, and the northern part of the Tohoku region on Honshu Island. We identified 2 cpDNA haplotypes, which represent not only populations on the Japan Sea coast but also those on the Pacific coast and this suggested the Okushiri Island populations might not be formed by single colonization. Genetic diversity of the Okushiri Island populations of nuclear SSR was not lower than the mainland and the STRUCTURE analysis revealed the Okushiri Island individuals were admixed between Hokkaido and Tohoku clusters. Approximate Bayesian computation inferred that divergence between Tohoku and Hokkaido, and admixture between two populations which generated Okushiri populations occurred before the last glacial maximum (LGM), that is, 7,890 (95% hyper probability density (HPD): 3,420 - 9,910) and 3,870 (95% HPD: 431- 8,540) generations ago, respectively. These inferences were well supported by a geological history which suggested an isolation of Okushiri Island from Hokkaido started prior to the Middle Pleistocene. We discuss the possible persistence of F. crenata during the last glacial maximum on northern islands in the Japan Sea such as Okushiri Island.
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Affiliation(s)
- Keiko Kitamura
- Hokkaido Research Centre, Forestry and Forest Products Research Institute, Sapporo, Japan
| | - Kanji Namikawa
- Biological Laboratory, Hokkaido University of Education, Sapporo, Japan
| | - Yoshiaki Tsuda
- Sugadaira Montane Research Center, University of Tsukuba, Ueda, Japan
| | - Makoto Kobayashi
- Department of Education and Culture, Echigo-Matsunoyama Museum of Natural Science, Tokamachi, Japan
| | - Tetsuya Matsui
- Center of Biodiversity and Climate Change, Forestry and Forest Products Research Institute, Tsukuba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Bang WJ, Ryu J, Kim YK, Won MH, Choi JW, Lee DY, Lee HS, Lee SY, Suh SJ, Choi KS. Two new records of insects (Arthropod: Insecta) from Dokdo Islands, Korea. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2021. [DOI: 10.1016/j.japb.2021.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Cho MS, Takayama K, Yang J, Maki M, Kim SC. Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation. FRONTIERS IN PLANT SCIENCE 2021; 12:706195. [PMID: 34539700 PMCID: PMC8445234 DOI: 10.3389/fpls.2021.706195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, South Korea
| | | | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Yun SA, Kim SC. Genetic diversity and structure of Saussurea polylepis (Asteraceae) on continental islands of Korea: Implications for conservation strategies and management. PLoS One 2021; 16:e0249752. [PMID: 33831066 PMCID: PMC8031399 DOI: 10.1371/journal.pone.0249752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 03/24/2021] [Indexed: 11/24/2022] Open
Abstract
Saussurea polylepis Nakai is an herbaceous perennial endemic to Korea and is highly restricted to several continental islands in the southwestern part of the Korean Peninsula. Given its very narrow geographical distribution, it is more vulnerable to anthropogenic activities and global climate changes than more widely distributed species. Despite the need for comprehensive genetic information for conservation and management, no such population genetic studies of S. polylepis have been conducted. In this study, genetic diversity and population structure were evaluated for 97 individuals from 5 populations (Gwanmaedo, Gageodo, Hongdo, Heusando, and Uido) using 19 polymorphic microsatellites. The populations were separated by a distance of 20–90 km. We found moderate levels of genetic diversity in S. polylepis (Ho = 0.42, He = 0.43). This may be due to long lifespans, outcrossing, and gene flow, despite its narrow range. High levels of gene flow (Nm = 1.76, mean Fst = 0.09), especially from wind-dispersed seeds, would contribute to low levels of genetic differentiation among populations. However, the small population size and reduced number of individuals in the reproductive phase of S. polylepis can be a major threat leading to inbreeding depression and genetic diversity loss. Bayesian cluster analysis revealed three significant structures at K = 3, consistent with DAPC and UPGMA. It is thought that sea level rise after the last glacial maximum may have acted as a geographical barrier, limiting the gene flow that would lead to distinct population structures. We proposed the Heuksando population, which is the largest island inhabited by S. polylepis, as a source population because of its large population size and high genetic diversity. Four management units (Gwanmaedo, Gageodo, Hongdo-Heuksando, and Uido) were suggested for conservation considering population size, genetic diversity, population structure, unique alleles, and geographical location (e.g., proximity).
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Affiliation(s)
- Seon A. Yun
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
- * E-mail: ,
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Gil HY, Maki M, Pimenova EA, Taran A, Kim SC. Origin of the critically endangered endemic species Scrophularia takesimensis (Scrophulariaceae) on Ulleung Island, Korea: implications for conservation. JOURNAL OF PLANT RESEARCH 2020; 133:765-782. [PMID: 32815044 DOI: 10.1007/s10265-020-01221-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed.
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Affiliation(s)
- Hee-Young Gil
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, South Korea
- DMZ Botanic Garden, Korea National Arboretum, 916-70, Punchbowl-ro, Haean-myeon, 24564, Yanggu, South Korea
| | - Masayuki Maki
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, 980-8578, Japan
| | | | - Aleksandr Taran
- Sakhalin Branch of Botanical Garden-Institute FEB RAS, Yuzhno-Sakhalinsk, Russia
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, South Korea.
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Park S, Park S. Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima. Sci Rep 2020; 10:16288. [PMID: 33004955 PMCID: PMC7529770 DOI: 10.1038/s41598-020-73397-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022] Open
Abstract
Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.,Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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Chloroplast DNA insights into the phylogenetic position and anagenetic speciation of Phedimus takesimensis (Crassulaceae) on Ulleung and Dokdo Islands, Korea. PLoS One 2020; 15:e0239734. [PMID: 32986762 PMCID: PMC7521733 DOI: 10.1371/journal.pone.0239734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/13/2020] [Indexed: 11/19/2022] Open
Abstract
Phedimus takesimensis (Ulleungdo flat-leaved stonecrop) is endemic to Ulleung and Dokdo Islands off the east coast of the Korean Peninsula. It was suggested that P. takesimensis originated via anagenetic speciation from the continental progenitor species P. kamtchaticus or P. aizoon. However, little is known of the phylogenetic relationships and population genetic structure among species of Phedimus in the Korean Peninsula and Ulleung/Dokdo Islands. We inferred the phylogenetic relationships among congeneric species in Korea based on nuclear ribosomal DNA internal transcribed spacer and chloroplast noncoding regions. We also sampled extensively for P. takesimensis on Ulleung Island and the continental species, P. kamtschaticus and P. aizoon, to assess the genetic consequences of anagenetic speciation. We found (1) the monophyly of P. takesimensis, (2) no apparent reduction in genetic diversity in anagenetically derived P. takesimensis compared to the continental progenitor species, (3) apparent population genetic structuring of P. takesimensis, and (4) two separate colonization events for the origin of the Dokdo Island population. This study contributes to our understanding of the genetic consequences of anagenetic speciation on Ulleung Island.
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Yang J, Kang GH, Pak JH, Kim SC. Characterization and Comparison of Two Complete Plastomes of Rosaceae Species ( Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea. Int J Mol Sci 2020; 21:E4933. [PMID: 32668601 PMCID: PMC7404287 DOI: 10.3390/ijms21144933] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 01/04/2023] Open
Abstract
Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 14 of the 75 protein-coding genes have been subject to strong purifying selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea;
| | - Gi-Ho Kang
- Baekdudaegan National Arboretum, 1501 Chunyang-ro, Chungyang-myeon, Bonghwa-gun, Gyeongsangbuk-do 36209, Korea;
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, Gyeongsangbuk-do 41566, Korea;
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon, Gyeonggi-do 16419, Korea
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Razafimandimbison SG, Kainulainen K, Senterre B, Morel C, Rydin C. Phylogenetic affinity of an enigmatic Rubiaceae from the Seychelles revealing a recent biogeographic link with Central Africa: gen. nov. Seychellea and trib. nov. Seychelleeae. Mol Phylogenet Evol 2019; 143:106685. [PMID: 31734453 DOI: 10.1016/j.ympev.2019.106685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 11/12/2019] [Indexed: 10/25/2022]
Abstract
The granitic islands of the Seychelles harbor about 268 native angiosperm species, with 28% being endemics there. The Seychelles biota contains a mix of ancient taxa with Gondwanan origins and young taxa that arrived there via dispersals. We investigate the phylogenetic position of an enigmatic, critically endangered, Seychellean endemic of the coffee family (Rubiaceae), Psathura/Psychotria sechellarum, and assess whether its presence on the granitic islands of the Seychelles is the result of vicariance or long-distance dispersal. Phylogenetic relationships of the family were reconstructed based on the Bayesian and maximum-likelihood phylogenetic analyses of sequence data from five plastid markers of 107 terminals. Divergence times were estimated using a Bayesian-based method. Psathura/Psychotria sechellarum is distantly related to Psychotria s.l. (including Psathura), and is strongly supported as sister to the Central African genus Colletoecema. Their striking morphological differences, coupled with their geographic separation and genetic distinctness, support the recognition of the new genus Seychellea and new tribe Seychelleeae to accommodate the Seychellean species. The Colletoecema-Seychellea clade constitutes an early-divergent lineage in the subfamily Rubioideae, with an old stem and a young crown ages estimated to be in the Late Cretaceous and late Oligocene-early Pliocene, respectively. Colletoecema diverged from Seychellea in the late Oligocene-early Pliocene and their respective crown ages are inferred to be late Miocene-middle Pleistocene and Pleistocene, respectively. The ancestor of the two genera was likely present in Africa, and reached the Seychelles via avian dispersal. Unlike Colletoecema with three species, Seychellea is monospecific, with very few individuals left in the wild. The species should be a top candidate for conservation priority, as its extinction would cause loss of genetic diversity of this entire lineage.
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Affiliation(s)
| | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottbergs Gata 22A, SE-41319 Gothenburg, Sweden
| | - Bruno Senterre
- Plant Conservation Action Group, P.O. Box 392, Victoria, Mahé, Seychelles; Island Biodiversity & Conservation Centre, Associated with the University of Seychelles, Anse Royale, Mahé P.O. Box 1348, Seychelles; Evolutionary Biology & Ecology - CP 160/12, Université Libre de Bruxelles, 50 Av. F. Roosevelt, 1050 Bruxelles, Belgium
| | - Charles Morel
- Seychelles National Herbarium, Bel Etang Building, Mont Feuri, Seychelles
| | - Catarina Rydin
- The Bergius Foundation, The Royal Swedish Academy of Sciences, Box 50005, SE-104 05 Stockholm, Sweden; Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Sugai K, Mori K, Murakami N, Kato H. Strong genetic structure revealed by microsatellite variation in Callicarpa species endemic to the Bonin (Ogasawara) Islands. JOURNAL OF PLANT RESEARCH 2019; 132:759-775. [PMID: 31625126 DOI: 10.1007/s10265-019-01144-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Adaptive radiation is the diversification of a founding population into multiple taxa that are differentially adapted to diverse ecological niches. The three Callicarpa (Lamiaceae) species endemic to the Bonin Islands are considered to represent an example of adaptive radiation on oceanic islands. All three species are distributed in the Chichijima Island Group and grow in different habitats, while only one species, C. subpubescens, is distributed among other island groups. Particularly, in the Hahajima and Mukojima Island Groups, C. subpubescens grows in various habitats and shows relatively high morphological variation. We investigated genotypes of the three Callicarpa species at 14 microsatellite markers to elucidate genetic differentiation within and between species or island groups and between different habitats or morphologies. We found that genetic differentiation within C. subpubescens in the Hahajima and Mukojima Island Groups was equally as high as that between the three species in the Chichijima Island Group, while differentiation within C. subpubescens in the Chichijima Island Group was much lower. Analyses such as a Bayesian clustering analysis showed that genetically distinct groups were associated with the three species in the Chichijima Island Group, whereas they showed strong genetic structure within C. subpubescens in the Hahajima and Mukojima Island Groups among different habitats and morphologies. These results indicated that ecological diversification occurred in the Hahajima and Mukojima Island Groups. Meanwhile, high genetic differentiation among different island groups was also observed, reflecting isolation by distance. It implies that non-ecological factors such as geographic isolation also played important roles in genetic differentiation in Callicarpa species in the Bonin Islands. These findings suggest that the Callicarpa species in the Bonin Islands are differentiated into multiple genetic groups by both ecological and non-ecological factors.
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Affiliation(s)
- Kyoko Sugai
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane, 690-8504, Japan.
| | - Keigo Mori
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Noriaki Murakami
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Hidetoshi Kato
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo, 192-0397, Japan
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Yang J, Pak JH, Maki M, Kim SC. Multiple origins and the population genetic structure of Rubus takesimensis (Rosaceae) on Ulleung Island: Implications for the genetic consequences of anagenetic speciation. PLoS One 2019; 14:e0222707. [PMID: 31536553 PMCID: PMC6752786 DOI: 10.1371/journal.pone.0222707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
To determine the origin and genetic consequences of anagenesis in Rubus takesimensis on Ulleung Island, Korea, we compared the genetic diversity and population structure of R. takesimensis with those of its continental progenitor R. crataegifolius. We broadly sampled a total of 315 accessions in 35 populations and sequenced five noncoding regions of chloroplast DNA. Rubus takesimensis emerged as nonmonophyletic and several geographically diverse continental populations were likely responsible for the origin of R. takesimensis; the majority of R. takesimensis accessions were sisters to the clade containing accessions of R. crataegifolius, primarily from the Korean peninsula, while rare accessions from three populations shared common ancestors with the ones from the southern part of the Korean peninsula, Jeju Island, and Japan. A few accessions from the Chusan population originated independently from the Korean peninsula. Of 129 haplotypes, 81 and 48 were found exclusively in R. crataegifolius and R. takesimensis, respectively. We found unusually high genetic diversity in two regions on Ulleung Island and no geographic population structure. For R. crataegifolius, two major haplotype groups were found; one for the northern mainland Korean peninsula, and the other for the southern Korean peninsula and the Japanese archipelago. Compared with populations of R. crataegifolius sampled from Japan, much higher haplotype diversity was found in populations from the Korean peninsula. The patterns of genetic consequences in R. takesimensis need to be verified for other endemic species based on chloroplast DNA and independent nuclear markers to synthesize emerging patterns of anagenetic speciation on Ulleung Island.
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Affiliation(s)
- JiYoung Yang
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Gyeongsangbuk-do, Korea
| | - Jae-Hong Pak
- Department of Biology, Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Gyeongsangbuk-do, Korea
- * E-mail: (SCK); (JHP)
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Sendai, Miyagi, Japan
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
- * E-mail: (SCK); (JHP)
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Chen Z, Lu X, Xuan Y, Tang F, Wang J, Shi D, Fu S, Ren J. Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum. BMC PLANT BIOLOGY 2019; 19:240. [PMID: 31170934 PMCID: PMC6555730 DOI: 10.1186/s12870-019-1850-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/28/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Red maple (Acer rubrum L.) is one of the most common and widespread trees with colorful leaves. We found a mutant with red, yellow, and green leaf phenotypes in different branches, which provided ideal materials with the same genetic relationship, and little interference from the environment, for the study of complex metabolic networks that underly variations in the coloration of leaves. We applied a combination of NGS and SMRT sequencing to various red maple tissues. RESULTS A total of 125,448 unigenes were obtained, of which 46 and 69 were thought to be related to the synthesis of anthocyanins and carotenoids, respectively. In addition, 88 unigenes were presumed to be involved in the chlorophyll metabolic pathway. Based on a comprehensive analysis of the pigment gene expression network, the mechanisms of leaf color were investigated. The massive accumulation of Cy led to its higher content and proportion than other pigments, which caused the redness of leaves. Yellow coloration was the result of the complete decomposition of chlorophyll pigments, the unmasking of carotenoid pigments, and a slight accumulation of Cy. CONCLUSIONS This study provides a systematic analysis of color variations in the red maple. Moreover, mass sequence data obtained by deep sequencing will provide references for the controlled breeding of red maple.
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Affiliation(s)
- Zhu Chen
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Xiaoyu Lu
- College of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 Anhui China
| | - Yun Xuan
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Fei Tang
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Jingjing Wang
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Dan Shi
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Songling Fu
- College of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036 Anhui China
| | - Jie Ren
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
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Kim JH, Quilantang NG, Kim HY, Lee S, Cho EJ. Attenuation of hydrogen peroxide-induced oxidative stress in SH-SY5Y cells by three flavonoids from Acer okamotoanum. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-018-0664-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Lee J, Yoon CY, Han E, Kim J. Development of 26 microsatellite markers in Bupleurum latissimum (Apiaceae), an endangered plant endemic to Ulleung Island, Korea. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1144. [PMID: 30131886 PMCID: PMC5947609 DOI: 10.1002/aps3.1144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/18/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY To enhance our understanding of evolutionary consequences and to establish a suitable conservation strategy, we isolated microsatellite markers for the endangered Bupleurum latissimum (Apiaceae), which is endemic to the oceanic Ulleung Island. We also attempted cross-amplification in B. euphorbioides and B. longeradiatum to investigate its continental progenitors. METHODS AND RESULTS Using high-throughput sequencing data, we developed 26 polymorphic microsatellite loci in three multiplexes, of which 13 loci were polymorphic in the two related species. For B. latissimum, alleles numbered two to four and the observed and expected heterozygosity ranged from 0.000 to 0.500 and 0.061 to 0.529, respectively. CONCLUSIONS These developed markers will be useful for understanding evolutionary patterns of B. latissimum in an oceanic island system and for establishing suitable conservation strategies at the genetic level.
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Affiliation(s)
- Jung‐Hyun Lee
- Department of Biology EducationChonnam National UniversityGwangju61186Korea
| | | | - Eun‐Kyeong Han
- Department of Biology EducationChonnam National UniversityGwangju61186Korea
| | - Joo‐Hwan Kim
- Department of Life ScienceGachon UniversitySeongnamdaero1342Seongnam‐siKorea
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16
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Graignic N, Tremblay F, Bergeron Y. Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple ( Acer saccharum Marshall). Ecol Evol 2018; 8:2766-2780. [PMID: 29531693 PMCID: PMC5838051 DOI: 10.1002/ece3.3906] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 12/03/2022] Open
Abstract
Due to climate change, the ranges of many North American tree species are expected to shift northward. Sugar maple (Acer saccharum Marshall) reaches its northern continuous distributional limit in northeastern North America at the transition between boreal mixed-wood and temperate deciduous forests. We hypothesized that marginal fragmented northern populations from the boreal mixed wood would have a distinct pattern of genetic structure and diversity. We analyzed variation at 18 microsatellite loci from 23 populations distributed along three latitudinal transects (west, central, and east) that encompass the continuous-discontinuous species range. Each transect was divided into two zones, continuous (temperate deciduous) and discontinuous (boreal mixed wood), based on sugar maple stand abundance. Respective positive and negative relationships were found between the distance of each population to the northern limit (D_north), and allelic richness (AR) and population differentiation (FST). These relations were tested for each transect separately; the pattern (discontinuous-continuous) remained significant only for the western transect. structure analysis revealed the presence of four clusters. The most northern populations of each transect were assigned to a distinct group. Asymmetrical gene flow occurred from the southern into the four northernmost populations. Southern populations in Québec may have originated from two different postglacial migration routes. No evidence was found to validate the hypothesis that northern populations were remnants of a larger population that had migrated further north of the species range after the retreat of the ice sheet. The northernmost sugar maple populations possibly originated from long-distance dispersal.
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Affiliation(s)
- Noémie Graignic
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
| | - Francine Tremblay
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
| | - Yves Bergeron
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
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17
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Tian X, Wang Q, Zhou Y. Euphorbia Section Hainanensis (Euphorbiaceae), a New Section Endemic to the Hainan Island of China From Biogeographical, Karyological, and Phenotypical Evidence. FRONTIERS IN PLANT SCIENCE 2018; 9:660. [PMID: 29868103 PMCID: PMC5968112 DOI: 10.3389/fpls.2018.00660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 04/30/2018] [Indexed: 05/18/2023]
Abstract
Euphorbia hainanensis is an endangered species endemic to the tropical Hainan Island in southern China and of historical importance for Chinese medicine. It is currently the only unplaced species of the genus Euphorbia (Euphorbiaceae) due to its isolated island distribution and debated placement by a previous molecular phylogenetic study. We sequenced nuclear ITS and chloroplast rbcL and ndhF for newly collected accessions of E. hainanensis and additional Euphorbia species found in Hainan, and analyzed the sequences in the context of the entire genus together with published data. All gene regions highly supported that E. hainanensis occupied an isolated phylogenetic position, showing no close affinity with any known Euphorbia sections suggesting it was a new section. ITS placed E. hainanensis sister to sect. Crossadenia (subgenus Chamaesyce) from Brazil with an estimated divergence time of 9.3-30.6 Mya while the chloroplast markers placed E. hainanensis at a position sister to the entire New World clade of Euphorbia subgenus Chamaesyce. In addition, our karyological results suggested a close affinity between E. hainanensis and the New World species of Euphorbia subg. Chamaesyce, with which shared the same chromosome number 2n = 28 and basic chromosome number x = 7. Phenotypically, E. hainanensis is unique with no close resemblance to other species in Euphorbia subg. Chamaesyce. Based on its isolated biogeographical, karyological, and phenotypical position, we propose a new section E. subgenus Chamaesyce section Hainanensis that might origin from long distance dispersal events because collective evidences showed a close affinity between the species from the Old World with those from the New World.
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Affiliation(s)
- Xinmin Tian
- Department of Biological Sciences, College of Life Science and Technology, Xinjiang University, Urumqi, China
- *Correspondence: Xinmin Tian
| | - Qiuyan Wang
- Key Laboratory of Oasis Ecology, Ministry of Education, Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, United States
- School of Life Science, Lanzhou University, Lanzhou, China
- Yongfeng Zhou
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18
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Gil HY, Kim SC. Viola woosanensis, a recurrent spontaneous hybrid between V. ulleungdoensis and V. chaerophylloides (Violaceae) endemic to Ulleung Island, Korea. JOURNAL OF PLANT RESEARCH 2016; 129:807-822. [PMID: 27206724 DOI: 10.1007/s10265-016-0830-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/23/2016] [Indexed: 06/05/2023]
Abstract
Ulleung Island is an oceanic volcanic island in Korea, which has never been connected to the adjacent continent. Previous studies highlighted Ulleung Island as an excellent system to study the pattern and process of early stages of flowering plant evolutions on oceanic island. The predominant mode of speciation in flowering plants on Ulleung Island appears to be anagenesis. However, the potentially important role of hybrid speciation among incompletely reproductively isolated lineages cannot be ruled out. Viola woosanensis (Violaceae) is of purportedly hybrid origin between V. ulleungdoensis (i.e., formerly recognized as V. selkirkii in Ulleung Island) and V. chaerophylloides, based on morphology. To examine the origin of V. woosanensis, we sampled a total of 80 accessions, including V. woosanensis and its putative parental species and sequenced nrDNA ITS, and four highly variable chloroplast noncoding regions (trnL-trnF, rpl16 intron, atpF-atpH, and psbA-trnH). Representative species of Viola from Korea were also included in the phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference). Additive polymorphic sites in the nrDNA ITS regions were confirmed by cloning amplicons from representative species. The molecular data strongly supported the hybrid origin of V. woosanensis, and the maternal and paternal parent were determined to be V. ulleungdoensis and V. chaerophylloides, respectively. The presence of two parental ribotypes in V. woosanensis (with the exception in one population) was confirmed by cloning, suggesting V. woosanensis is primarily the F1 generation. No trace of backcrossing and introgression with its parents was detected due to low fertility of hybrid species. We found a multiple and unidirectional hybrid origin of V. woosanensis. Additional studies are required to determine which factors contribute to asymmetric gene flow of Viola species in Ulleung Island.
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Affiliation(s)
- Hee-Young Gil
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-Do, 16419, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-Do, 16419, Korea.
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19
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Graignic N, Tremblay F, Bergeron Y. Genetic consequences of selection cutting on sugar maple (Acer saccharum Marshall). Evol Appl 2016; 9:777-90. [PMID: 27330554 PMCID: PMC4908464 DOI: 10.1111/eva.12384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/10/2016] [Indexed: 11/30/2022] Open
Abstract
Selection cutting is a treatment that emulates tree-by-tree replacement for forests with uneven-age structures. It creates small openings in large areas and often generates a more homogenous forest structure (fewer large leaving trees and defective trees) that differs from old-growth forest. In this study, we evaluated whether this type of harvesting has an impact on genetic diversity of sugar maple (Acer saccharum Marshall). Genetic diversity among seedlings, saplings, and mature trees was compared between selection cut and old-growth forest stands in Québec, Canada. We found higher observed heterozygosity and a lower inbreeding coefficient in mature trees than in younger regeneration cohorts of both forest types. We detected a recent bottleneck in all stands undergoing selection cutting. Other genetic indices of diversity (allelic richness, observed and expected heterozygosity, and rare alleles) were similar between forest types. We concluded that the effect of selection cutting on the genetic diversity of sugar maple was recent and no evidence of genetic erosion was detectable in Québec stands after one harvest. However, the cumulative effect of recurring applications of selection cutting in bottlenecked stands could lead to fixation of deleterious alleles, and this highlights the need for adopting better forest management practices.
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Affiliation(s)
- Noémie Graignic
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
| | - Francine Tremblay
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
| | - Yves Bergeron
- Institut de Recherche sur les ForêtsUniversité du Québec en Abitibi‐TémiscamingueRouyn‐NorandaQCCanada
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20
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Kaya S, Çiplak B. Budding speciation via peripheral isolation: thePsorodonotus venosus(Orthoptera, Tettigoniidae) species group example. ZOOL SCR 2016. [DOI: 10.1111/zsc.12174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sarp Kaya
- Department of Biology; Faculty of Science; Akdeniz University Antalya; Antalya Turkey
| | - Battal Çiplak
- Department of Biology; Faculty of Science; Akdeniz University Antalya; Antalya Turkey
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21
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Takayama K, López-Sepúlveda P, Greimler J, Crawford DJ, Peñailillo P, Baeza M, Ruiz E, Kohl G, Tremetsberger K, Gatica A, Letelier L, Novoa P, Novak J, Stuessy TF. Genetic consequences of cladogenetic vs. anagenetic speciation in endemic plants of oceanic islands. AOB PLANTS 2015; 7:plv102. [PMID: 26311732 PMCID: PMC4605995 DOI: 10.1093/aobpla/plv102] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 07/27/2015] [Indexed: 05/27/2023]
Abstract
Adaptive radiation is a common mode of speciation among plants endemic to oceanic islands. This pattern is one of cladogenesis, or splitting of the founder population, into diverse lineages in divergent habitats. In contrast, endemic species have also evolved primarily by simple transformations from progenitors in source regions. This is anagenesis, whereby the founding population changes genetically and morphologically over time primarily through mutation and recombination. Gene flow among populations is maintained in a homogeneous environment with no splitting events. Genetic consequences of these modes of speciation have been examined in the Juan Fernández Archipelago, which contains two principal islands of differing geological ages. This article summarizes population genetic results (nearly 4000 analyses) from examination of 15 endemic species, involving 1716 and 1870 individuals in 162 and 163 populations (with amplified fragment length polymorphisms and simple sequence repeats, respectively) in the following genera: Drimys (Winteraceae), Myrceugenia (Myrtaceae), Rhaphithamnus (Verbenaceae), Robinsonia (Asteraceae, Senecioneae) and Erigeron (Asteraceae, Astereae). The results indicate that species originating anagenetically show high levels of genetic variation within the island population and no geographic genetic partitioning. This contrasts with cladogenetic species that show less genetic diversity within and among populations. Species that have been derived anagenetically on the younger island (1-2 Ma) contain less genetic variation than those that have anagenetically speciated on the older island (4 Ma). Genetic distinctness among cladogenetically derived species on the older island is greater than among similarly derived species on the younger island. An important point is that the total genetic variation within each genus analysed is comparable, regardless of whether adaptive divergence occurs.
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Affiliation(s)
- Koji Takayama
- Museum of Natural and Environmental History, Shizuoka, Oya 5762, Suruga-ku, Shizuoka-shi, Shizuoka 422-8017, Japan
| | | | - Josef Greimler
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Daniel J Crawford
- Department of Ecology and Evolutionary Biology and the Biodiversity Institute, University of Kansas, Lawrence, KS 60045, USA
| | - Patricio Peñailillo
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Marcelo Baeza
- Departamento de Botánica, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Eduardo Ruiz
- Departamento de Botánica, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Gudrun Kohl
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Karin Tremetsberger
- Institute of Botany, Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, A-1180 Vienna, Austria
| | - Alejandro Gatica
- Bioma Consultores S.A., Mariano Sanchez Fontecilla No. 396, Las Condes, Santiago, Chile
| | - Luis Letelier
- Universidad Bernardo O'Higgins, Centro de Investigaciones en Recursos Naturales y Sustentabilidad, General Gana 1702, Santiago, Chile
| | - Patricio Novoa
- Jardín Botánico de Viña del Mar, Corporación Nacional Forestal, Camino El Olivar 305, Viña del Mar, Chile
| | - Johannes Novak
- Institute for Applied Botany and Pharmacognosy, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Tod F Stuessy
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria Herbarium, Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA
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22
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Li L, Sun Y, Zou J, Yue W, Wang X, Liu J. Origin and speciation of Picea schrenkiana and Piceasmithiana in the Center Asian Highlands and Himalayas. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:661-672. [PMID: 25999663 PMCID: PMC4432025 DOI: 10.1007/s11105-014-0774-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of Picea schrenkiana and Picea smithiana using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with Picea likiangensis or Picea wilsonii which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, P. schrenkiana appeared to be closely related to P. likiangensis, although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that P. schrenkiana and P. smithiana are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the P. likiangensis-P. wilsonii clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands.
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Affiliation(s)
- Lili Li
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Yongshuai Sun
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Jiabin Zou
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Wei Yue
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Xi Wang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000 China
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23
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García-Verdugo C, Sajeva M, La Mantia T, Harrouni C, Msanda F, Caujapé-Castells J. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates. Mol Ecol 2015; 24:726-41. [PMID: 25580539 DOI: 10.1111/mec.13060] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/16/2014] [Accepted: 12/30/2014] [Indexed: 01/17/2023]
Abstract
Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.
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Affiliation(s)
- C García-Verdugo
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
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24
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Takayama K, López-Sepúlveda P, Greimler J, Crawford DJ, Peñailillo P, Baeza M, Ruiz E, Kohl G, Tremetsberger K, Gatica A, Letelier L, Novoa P, Novak J, Stuessy TF. Relationships and genetic consequences of contrasting modes of speciation among endemic species of Robinsonia (Asteraceae, Senecioneae) of the Juan Fernández Archipelago, Chile, based on AFLPs and SSRs. THE NEW PHYTOLOGIST 2015; 205:415-28. [PMID: 25209139 DOI: 10.1111/nph.13000] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/14/2014] [Indexed: 05/23/2023]
Abstract
This study analyses and compares the genetic signatures of anagenetic and cladogenetic speciation in six species of the genus Robinsonia (Asteraceae, Senecioneae), endemic to the Juan Fernández Islands, Chile. Population genetic structure was analyzed by amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) markers from 286 and 320 individuals, respectively, in 28 populations. Each species is genetically distinct. Previous hypotheses of classification among these species into subgenera and sections, via morphological, phytochemical, isozymic and internal transcribed spacer (ITS) data, have been confirmed, except that R. saxatilis appears to be related to R. gayana rather than R. evenia. Analysis of phylogenetic results and biogeographic context suggests that five of these species have originated by cladogenesis and adaptive radiation on the older Robinson Crusoe Island. The sixth species, R. masafuerae, restricted to the younger Alejandro Selkirk Island, is closely related to and an anagenetic derivative of R. evenia from Robinson Crusoe. Microsatellite and AFLP data reveal considerable genetic variation among the cladogenetically derived species of Robinsonia, but within each the genetic variation is lower, highlighting presumptive genetic isolation and rapid radiation. The anagenetically derived R. masafuerae harbors a level of genetic variation similar to that of its progenitor, R. evenia. This is the first direct comparison of the genetic consequences of anagenetic and cladogenetic speciation in plants of an oceanic archipelago.
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Affiliation(s)
- Koji Takayama
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan
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25
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López-Sepúlveda P, Takayama K, Greimler J, Crawford DJ, Peñailillo P, Baeza M, Ruiz E, Kohl G, Tremetsberger K, Gatica A, Letelier L, Novoa P, Novak J, Stuessy TF. Progressive migration and anagenesis in Drimys confertifolia of the Juan Fernández Archipelago, Chile. JOURNAL OF PLANT RESEARCH 2015; 128:73-90. [PMID: 25292282 PMCID: PMC4300435 DOI: 10.1007/s10265-014-0666-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/12/2014] [Indexed: 05/23/2023]
Abstract
A common mode of speciation in oceanic islands is by anagenesis, wherein an immigrant arrives and through time transforms by mutation, recombination, and drift into a morphologically and genetically distinct species, with the new species accumulating a high level of genetic diversity. We investigate speciation in Drimys confertifolia, endemic to the two major islands of the Juan Fernández Archipelago, Chile, to determine genetic consequences of anagenesis, to examine relationships among populations of D. confertifolia and the continental species D. winteri and D. andina, and to test probable migration routes between the major islands. Population genetic analyses were conducted using AFLPs and nuclear microsatellites of 421 individuals from 42 populations from the Juan Fernández islands and the continent. Drimys confertifolia shows a wide genetic variation within populations on both islands, and values of genetic diversity within populations are similar to those found within populations of the continental progenitor. The genetic results are compatible with the hypothesis of high levels of genetic variation accumulating within anagenetically derived species in oceanic islands, and with the concept of little or no geographical partitioning of this variation over the landscape. Analysis of the probability of migration within the archipelago confirms colonization from the older island, Robinson Crusoe, to the younger island Alejandro Selkirk.
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Affiliation(s)
| | - Koji Takayama
- The University Museum, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Josef Greimler
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Daniel J. Crawford
- Department of Ecology and Evolutionary Biology and the Biodiversity Institute, University of Kansas, Lawrence, KS 60045, USA
| | - Patricio Peñailillo
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Marcelo Baeza
- Departamento de Botánica, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Eduardo Ruiz
- Departamento de Botánica, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Gudrun Kohl
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of Vienna, Rennweg 14, 1030 Vienna, Austria
| | - Karin Tremetsberger
- Department of Integrative Biology and Biodiversity Research, Institute of Botany, University of Natural Resources and Life Sciences, Gregor Mendel Straße 33, 1180 Vienna, Austria
| | - Alejandro Gatica
- Laboratorio de Ecofisiología Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad de La Serena, Casilla 599, La Serena, Chile
| | - Luis Letelier
- Centro de Investigaciones en Ecosistemas, Universidad Nacional Autónoma de México, C.P. 58190 Morelia, Michoacán Mexico
| | - Patricio Novoa
- Jardín Botánico de Viña del Mar, Corporación Nacional Forestal, Camino El Olivar 305, Viña del Mar, Chile
| | - Johannes Novak
- Institute for Applied Botany and Pharmacognosy, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Tod F. Stuessy
- Herbarium, Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 1315 Kinnear Road, Columbus, OH 43212, USA
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26
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Stuessy TF, Takayama K, López-Sepúlveda P, Crawford DJ. Interpretation of patterns of genetic variation in endemic plant species of oceanic islands. BOTANICAL JOURNAL OF THE LINNEAN SOCIETY. LINNEAN SOCIETY OF LONDON 2014; 174:276-288. [PMID: 26074627 PMCID: PMC4459035 DOI: 10.1111/boj.12088] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/18/2013] [Accepted: 07/07/2013] [Indexed: 05/07/2023]
Abstract
Oceanic islands offer special opportunities for understanding the patterns and processes of evolution. The availability of molecular markers in recent decades has enhanced these opportunities, facilitating the use of population genetics to reveal divergence and speciation in island systems. A common pattern seen in taxa on oceanic islands is a decreased level of genetic variation within and among populations, and the founder effect has often been invoked to explain this observation. Founder effects have a major impact on immigrant populations, but, over millions of years, the original genetic signature will normally be erased as a result of mutation, recombination, drift and selection. Therefore, the types and degrees of genetic modifications that occur must often be caused by other factors, which should be considered when explaining the patterns of genetic variation. The age of the island is extremely important because oceanic islands subside on their submarine plates over time. Erosion caused by wind, rain and wave action combine to grind down soft volcanic substrates. These geomorphological events can have a dramatic impact on population number and size, and hence levels of genetic diversity. The mode of speciation is also of significance. With anagenesis, genetic variation accumulates through time, whereas, with cladogenenesis, the gene pool splits into populations of adaptively radiating species. Breeding systems, population sizes and generation times are also important, as is hybridization between closely related taxa. Human disturbance has affected plant population number and size through the harvesting of forests and the introduction of invasive plants and animals. Therefore, the explanation of the observed levels of genetic variation in species of oceanic islands requires the consideration of many interconnected physical, biological and anthropomorphic factors.
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Affiliation(s)
- Tod F Stuessy
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of ViennaRennweg 14, A-1030, Vienna, Austria
- *Corresponding author. E-mail:
| | - Koji Takayama
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of ViennaRennweg 14, A-1030, Vienna, Austria
| | - Patricio López-Sepúlveda
- Department of Systematic and Evolutionary Botany, Biodiversity Center, University of ViennaRennweg 14, A-1030, Vienna, Austria
| | - Daniel J Crawford
- Department of Ecology & Evolutionary Biology and the Biodiversity Institute, University of KansasLawrence, KS, 66045, USA
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27
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Zou J, Sun Y, Li L, Wang G, Yue W, Lu Z, Wang Q, Liu J. Population genetic evidence for speciation pattern and gene flow between Picea wilsonii, P. morrisonicola and P. neoveitchii. ANNALS OF BOTANY 2013; 112:1829-44. [PMID: 24220103 PMCID: PMC3838563 DOI: 10.1093/aob/mct241] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/30/2013] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of spruce with similar morphology, Picea wilsonii, P. neoveitchii and P. morrisonicola. Picea wilsonii and P. neoveitchii occur from central to north-west China, where they have overlapping distributions. Picea morrisonicola, however, is restricted solely to the island of Taiwan and is isolated from the other two species by a long distance. METHODS Sequence variations were examined in 18 DNA fragments for 22 populations, including three fragments from the chloroplast (cp) genome, two from the mitochondrial (mt) genome and 13 from the nuclear genome. KEY RESULTS In both the cpDNA and the mtDNA, P. morrisonicola accumulated more species-specific mutations than the other two species. However, most nuclear haplotypes of P. morrisonicola were shared by P. wilsonii, or derived from the dominant haplotypes found in that species. Modelling of population genetic data supported the hypothesis that P. morrisonicola derived from P. wilsonii within the more recent past, most probably indicating progenitor-derivative speciation with a distinct bottleneck, although further gene flow from the progenitor to the derivative continued. In addition, the occurrence was detected of an obvious mtDNA introgression from P. neoveitchii to P. wilsonii despite their early divergence. CONCLUSIONS The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species.
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Affiliation(s)
| | | | | | | | | | | | | | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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