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Ortiz D, Pekár S, Dianat M. A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders. Mol Phylogenet Evol 2024; 199:108167. [PMID: 39103025 DOI: 10.1016/j.ympev.2024.108167] [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: 04/29/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
Disentangling the genomic intricacies underlying speciation and the causes of discordance between sources of evidence can offer remarkable insights into evolutionary dynamics. The ant-eating spider Zodarion nitidum, found across the Middle East and Egypt, displays yellowish and blackish morphs that co-occur sympatrically. These morphs additionally differ in behavioral and physiological features and show complete pre-mating reproductive isolation. In contrast, they possess similar sexual features and lack distinct differences in their mitochondrial DNA. We analyzed both Z. nitidum morphs and outgroups using genome-wide and additional mitochondrial DNA data. The genomic evidence indicated that Yellow and Black are reciprocally independent lineages without signs of recent admixture. Interestingly, the sister group of Yellow is not Black but Z. luctuosum, a morphologically distinct species. Genomic gene flow analyses pinpointed an asymmetric nuclear introgression event, with Yellow contributing nearly 5 % of its genome to Black roughly 320,000 years ago, intriguingly aligning with the independently estimated origin of the mitochondrial DNA of Black. We conclude that the blackish and yellowish morphs of Z. nitidum are long-diverged distinct species, and that the ancient and modest genomic introgression event registered resulted in a complete mitochondrial takeover of Black by Yellow. This investigation underscores the profound long-term effects that even modest hybridization events can have on the genome of organisms. It also exemplifies the utility of phylogenetic networks for estimating historical events and how integrating independent lines of evidence can increase the reliability of such estimations.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Malahat Dianat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia
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Ye H, Wang Y, Liu H, Lei D, Li H, Gao Z, Feng X, Han M, Qie Q, Zhou H. The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1334. [PMID: 38794406 PMCID: PMC11125379 DOI: 10.3390/plants13101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.
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Affiliation(s)
- Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yiling Wang
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Dingfan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhimei Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaolong Feng
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Mian Han
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Qiyang Qie
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, China
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Lü Z, Liu T, Liu Y, Wang Y, Liu J, Liu B, Gong L, Liu L. Climate Adaptation and Drift Shape the Genomes of Two Eel-Goby Sister Species Endemic to Contrasting Latitude. Animals (Basel) 2023; 13:3240. [PMID: 37893964 PMCID: PMC10603712 DOI: 10.3390/ani13203240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Deciphering the role of climate adaptation in generating genetic divergence and hence speciation is a central question in evolution. Comparisons of genomes of closely related species spanning selective climate gradients are particularly informative in discerning the signatures of selection and thereby providing valuable information concerning the role of climate adaptation in speciation. Here we re-sequenced 99 genomes of the two sister eel-goby species Odontamblyopus lacepedii and O. rebecca, which are endemic to tidal mudflats spanning contrasting latitude gradients, to estimate the influence of divergent climate selection on shaping genome-wide patterns of divergence. The results indicated that genome-wide differentiation between the two species was evident (genome-wide FST = 0.313). Against a background of high baseline genomic divergence, 588 and 1202 elevated divergent loci were detected to be widespread throughout their genomes, as opposed to focused within small islands of genomic regions. These patterns of divergence may arise from divergent climate selection in addition to genetic drift acting through past glacial segregation (1.46 million years ago). We identified several candidate genes that exhibited elevated divergence between the two species, including genes associated with substance metabolism, energy production, and response to environmental cues, all putative candidates closely linked to thermal adaptation expected from the latitude gradient. Interestingly, several candidates related to gamete recognition and time of puberty, and also exhibited elevated divergence, indicating their possible role in pre-zygote isolation and speciation of the two species. Our results would expand our knowledge on the roles of latitude climate adaptation and genetic drift in generating and maintaining biodiversity in marine teleosts.
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Affiliation(s)
- Zhenming Lü
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Tianwei Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Yantao Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Yuzhen Wang
- National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China;
| | - Jing Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
| | - Liqin Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, College of Marine Sciences and Technology, Zhejiang Ocean University, Zhoushan 316022, China; (Z.L.); (T.L.); (Y.L.); (J.L.); (B.L.); (L.G.)
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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.
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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
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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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Dong F, Li SH, Chiu CC, Dong L, Yao CT, Yang XJ. Strict allopatric speciation of sky island Pyrrhula erythaca species complex. Mol Phylogenet Evol 2020; 153:106941. [PMID: 32818596 DOI: 10.1016/j.ympev.2020.106941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 07/01/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Increasing evidence of post-divergence gene flow between taxa is shifting our understanding on the mode of speciation. A fundamental question arises concerning the circumstances under which strict allopatric speciation still holds true. Sky island populations might undergo reduced gene flow by niche conservatism to highland habitats and follow divergence in an allopatric manner. In this study, we tested this hypothesis in the sky island Grey-headed Bullfinch (Pyrrhula erythaca) species complex via statistical analyses of both genetic and ecological data. Results of coalescent-based analysis of multiple nuclear loci suggested that P. e. owstoni likely colonized Taiwan island during the severe mid-Pleistocene glacial climate followed by strictly allopatric divergence from P. e. erythaca distributed in Himalayas-Hengduan mountains and central North China. Results of ecological niche modeling suggested that their speciation may be attributed to the niche conservatism of these birds and the lack of a suitable ecological corridor during subsequent milder glacial episodes. In addition, we delimited the traditionally defined P. erythaca into two full species, P. erythaca in the Asian mainland and P. owstoni on the island of Taiwan, based on both genetic and behavioural evidences. These results suggest that ecology can have a dynamic role in allowing highland populations to expand their ranges and isolated by habitat barriers to diversify in a strictly allopatric manner.
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Affiliation(s)
- Feng Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Chi-Cheng Chiu
- Department of Life Science, National Taiwan Normal University, Taipei 116, Taiwan
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Endemic Species Research Institute, Minsheng East Road, Jiji Township, Nantou County 552, Taiwan.
| | - Xiao-Jun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
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Dong F, Hung CM, Yang XJ. Secondary contact after allopatric divergence explains avian speciation and high species diversity in the Himalayan-Hengduan Mountains. Mol Phylogenet Evol 2020; 143:106671. [DOI: 10.1016/j.ympev.2019.106671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 11/25/2022]
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Zeng YF, Zhang JG, Abuduhamiti B, Wang WT, Jia ZQ. Phylogeographic patterns of the desert poplar in Northwest China shaped by both geology and climatic oscillations. BMC Evol Biol 2018; 18:75. [PMID: 29801429 PMCID: PMC5970483 DOI: 10.1186/s12862-018-1194-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 05/17/2018] [Indexed: 12/15/2022] Open
Abstract
Background The effects of historical geology and climatic events on the evolution of plants around the Qinghai-Tibetan Plateau region have been at the center of debate for years. To identify the influence of the uplift of the Tianshan Mountains and/or climatic oscillations on the evolution of plants in arid northwest China, we investigated the phylogeography of the Euphrates poplar (Populus euphratica) using chloroplast DNA (cpDNA) sequences and nuclear microsatellites, and estimated its historical distribution using Ecological Niche Modeling (ENM). Results We found that the Euphrates poplar differed from another desert poplar, P. pruinosa, in both nuclear and chloroplast DNA. The low clonal diversity in both populations reflected the low regeneration rate by seed/seedlings in many locations. Both cpDNA and nuclear markers demonstrated a clear divergence between the Euphrates poplar populations from northern and southern Xinjiang regions. The divergence time was estimated to be early Pleistocene based on cpDNA, and late Pleistocene using an Approximate Bayesian Computation analysis based on microsatellites. Estimated gene flow was low between these two regions, and the limited gene flow occurred mainly via dispersal from eastern regions. ENM analysis supported a wider distribution of the Euphrates poplar at 3 Ma, but a more constricted distribution during both the glacial period and the interglacial period. Conclusions These results indicate that the deformation of the Tianshan Mountains has impeded gene flow of the Euphrates poplar populations from northern and southern Xinjiang, and the distribution constriction due to climatic oscillations further accelerated the divergence of populations from these regions. To protect the desert poplars, more effort is needed to encourage seed germination and seedling establishment, and to conserve endemic gene resources in the northern Xinjiang region. Electronic supplementary material The online version of this article (10.1186/s12862-018-1194-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan-Fei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, NO. 1 Dongxiaofu, Xiangshan road, Haidian district, Beijing, 100091, China
| | - Jian-Guo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, NO. 1 Dongxiaofu, Xiangshan road, Haidian district, Beijing, 100091, China. .,Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, No. 159 Longpan road, Nanjing, 210037, China. .,Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan road, Haidian district, Beijing, 100091, China.
| | - Bawerjan Abuduhamiti
- Forest Research Institute of the Altai Region, No. 93 Jiefang South Road, Altai, Xinjiang, 836500, China
| | - Wen-Ting Wang
- School of Mathematics and Computer Science, Northwest University for Nationalities, No. 1 Northwest new village, Lanzhou, 730030, Gansu, China
| | - Zhi-Qing Jia
- Institute of Desertification Studies, Chinese Academy of Forestry, Xiangshan road, Haidian district, Beijing, 100091, China
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Bai WN, Yan PC, Zhang BW, Woeste KE, Lin K, Zhang DY. Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences. THE NEW PHYTOLOGIST 2018; 217:1726-1736. [PMID: 29178135 DOI: 10.1111/nph.14917] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/24/2017] [Indexed: 05/18/2023]
Abstract
Whether species demography and diversification are driven primarily by extrinsic environmental changes such as climatic oscillations in the Quaternary or by intrinsic biological interactions like coevolution between antagonists is a matter of active debate. In fact, their relative importance can be assessed by tracking past population fluctuations over considerable time periods. We applied the pairwise sequentially Markovian coalescent approach on the genomes of 11 temperate Juglans species to estimate trajectories of changes in effective population size (Ne ) and used a Bayesian-coalescent based approach that simultaneously considers multiple genomes (G-PhoCS) to estimate divergence times between lineages. Ne curves of all study species converged 1.0 million yr ago, probably reflecting the time when the walnut genus last shared a common ancestor. This estimate was confirmed by the G-PhoCS estimates of divergence times. But all species did not react similarly to the dramatic climatic oscillations following early Pleistocene cooling, so the timing and amplitude of changes in Ne differed among species and even among conspecific lineages. The population histories of temperate walnut species were not driven by extrinsic environmental changes alone, and a key role was probably played by species-specific factors such as coevolutionary interactions with specialized pathogens.
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Affiliation(s)
- Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Peng-Cheng Yan
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, 100094, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Keith E Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex. Proc Natl Acad Sci U S A 2017; 115:E236-E243. [PMID: 29279400 PMCID: PMC5777044 DOI: 10.1073/pnas.1713288114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
One of the outstanding questions in understanding how new species form is how reproductive isolation arises. In particular, the relative roles of gene flow and natural selection in creating two separate species remains open for debate. Here we show within the four continuously speciating lineages of a poplar that local genomic differentiation of populations is not associated with either rate of recent gene flow or time of species divergence. By contrast, we found that these genomic islands of divergence most likely came about by selective processes—sorting of ancient genetic polymorphisms and the incidental hitchhiking of linked variations. These findings substantially enhance our understanding of genomic changes in speciation. How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.
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Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva JAP, Dossat C, Aury JM, Plomion C, Kremer A. Extensive recent secondary contacts between four European white oak species. THE NEW PHYTOLOGIST 2017; 214:865-878. [PMID: 28085203 PMCID: PMC5624484 DOI: 10.1111/nph.14413] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/21/2016] [Indexed: 05/04/2023]
Abstract
Historical trajectories of tree species during the late Quaternary have been well reconstructed through genetic and palaeobotanical studies. However, many congeneric tree species are interfertile, and the timing and contribution of introgression to species divergence during their evolutionary history remains largely unknown. We quantified past and current gene flow events between four morphologically divergent oak species (Quercus petraea, Q. robur, Q. pyrenaica, Q. pubescens), by two independent inference methods: diffusion approximation to the joint frequency spectrum (∂a∂i) and approximate Bayesian computation (ABC). For each pair of species, alternative scenarios of speciation allowing gene flow over different timescales were evaluated. Analyses of 3524 single nucleotide polymorphisms (SNPs) randomly distributed in the genome, showed that these species evolved in complete isolation for most of their history, but recently came into secondary contact, probably facilitated by the most recent period of postglacial warming. We demonstrated that: there was sufficient genetic differentiation before secondary contact for the accumulation of barriers to gene flow; and current European white oak genomes are a mosaic of genes that have crossed species boundaries and genes impermeable to gene flow.
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Affiliation(s)
- Thibault Leroy
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| | - Camille Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Laure Villate
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
| | | | - Jonathan Romiguier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jorge A P Paiva
- Instituto de Biologia Experimental e Tecnológica, iBET, Apartado 12, Oeiras, 2780-901, Portugal
- Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszynska street, Poznań, PL-60-479, Poland
| | - Carole Dossat
- Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France
| | - Jean-Marc Aury
- Institut de Genomique (IG), Commissariat à l'Energie Atomique (CEA), Genoscope, Evry, 91057, France
| | | | - Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, Cestas, 33610, France
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12
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Zheng H, Fan L, Milne RI, Zhang L, Wang Y, Mao K. Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China. FRONTIERS IN PLANT SCIENCE 2017; 8:375. [PMID: 28377782 PMCID: PMC5359289 DOI: 10.3389/fpls.2017.00375] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/06/2017] [Indexed: 05/13/2023]
Abstract
Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary history.
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Affiliation(s)
- Honglei Zheng
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Liqiang Fan
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Yaling Wang
- Life Science and Engineering College, Northwest University for NationalitiesLanzhou, China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
- *Correspondence: Kangshan Mao ;
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13
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Wu Y, Meng K, Liang X. Distinct patterns of natural selection in Na +/H + antiporter genes in Populus euphratica and Populus pruinosa. Ecol Evol 2016; 7:82-91. [PMID: 28070277 PMCID: PMC5214168 DOI: 10.1002/ece3.2639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/17/2016] [Accepted: 10/19/2016] [Indexed: 01/28/2023] Open
Abstract
Salt tolerance genes constitute an important class of loci in plant genomes. Little is known about the extent to which natural selection in saline environments has acted upon these loci, and what types of nucleotide diversity such selection has given rise to. Here, we surveyed genetic diversity in three types of Na+/H+ antiporter gene (SOS, NhaD, and NHX, belonging to the cation/proton antiporter 1 family), which have well‐characterized essential roles in plant salt tolerance. Ten Na+/H+ antiporter genes and 16 neutral loci randomly selected as controls were sequenced from 17 accessions of two closely related members of the genus Populus, Populus euphratica and Populus pruinosa, section Turanga, which are native to northwest China. The results show that salt tolerance genes are common targets of natural selection in P. euphratica and P. pruinosa. Moreover, the patterns of nucleotide variation across the three types of Na+/H+ antiporter gene are distinctly different in these two closely related Populus species, and gene flow from P. pruinosa to P. euphratica is highly restricted. Our results suggest that natural selection played an important role in shaping the current distinct patterns of Na+/H+ antiporter genes, resulting in adaptive evolution in P. euphratica and P. pruinosa.
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Affiliation(s)
- Yuxia Wu
- State Key Laboratory of Grassland Agro-Ecosystem School of Life Sciences Lanzhou University Lanzhou Gansu China
| | - Kuibin Meng
- State Key Laboratory of Grassland Agro-Ecosystem School of Life Sciences Lanzhou University Lanzhou Gansu China
| | - Xiaohui Liang
- State Key Laboratory of Grassland Agro-Ecosystem School of Life Sciences Lanzhou University Lanzhou Gansu China
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14
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Ma J, He X, Bai X, Niu Z, Duan B, Chen N, Shao X, Wan D. Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars. Genes (Basel) 2016; 7:genes7120111. [PMID: 27916935 PMCID: PMC5192487 DOI: 10.3390/genes7120111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/24/2016] [Accepted: 11/24/2016] [Indexed: 11/16/2022] Open
Abstract
Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xiaodong He
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Bingbing Duan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Ningning Chen
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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15
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Yoichi W, Tamaki I, Sakaguchi S, Song JS, Yamamoto SI, Tomaru N. Population demographic history of a temperate shrub, Rhododendron weyrichii (Ericaceae), on continental islands of Japan and South Korea. Ecol Evol 2016; 6:8800-8810. [PMID: 28035270 PMCID: PMC5192946 DOI: 10.1002/ece3.2576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 11/04/2016] [Accepted: 10/06/2016] [Indexed: 01/18/2023] Open
Abstract
Continental islands provide opportunities for testing the effects of isolation and migration on genetic variation in plant populations. In characteristic of continental islands is that the geographic connections between these islands, which are currently distinguished by seaways, have experienced fluctuations caused by sea‐level changes due to climate oscillations during the Quaternary. Plant populations on the islands have migrated between these islands via the exposed seafloors or been isolated. Here, we examined the demographic history of a temperate shrub, Rhododendron weyrichii, which is distributed in the southwestern parts of the Japanese archipelago and on an island of South Korea, using statistical phylogeographic approaches based on the DNA sequences of two chloroplast and eight nuclear loci in samples analyzed from 18 populations on eight continental islands, and palaeodistribution modeling. Time estimates for four island populations indicate that the durations of vicariance history are different between these populations, and these events have continued since the last glacial or may have predated the last glacial. The constancy or expansion of population sizes on the Japanese islands, and in contrast a bottleneck in population size on the Korean island Jeju, suggests that these islands may have provided different conditions for sustaining populations. The result of palaeodistribution modeling indicates that the longitudinal range of the species as a whole has not changed greatly since the last glacial maximum. These results indicate that exposed seafloors during the glacial period formed both effective and ineffective migration corridors. These findings may shed light on the effects of seafloor exposure on the migration of plants distributed across continental islands.
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Affiliation(s)
- Watanabe Yoichi
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan; Present address: Graduate School of Horticulture Chiba University Matsudo 648 Matsudo Chiba 271-8510 Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture Mino Gifu Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
| | - Jong-Suk Song
- Department of Biological Science College of Natural Sciences Andong National University Andong Gyeongbuk Korea
| | | | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
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16
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Martín-Bravo S, Daniel TF. Molecular evidence supports ancient long-distance dispersal for the amphi-Atlantic disjunction in the giant yellow shrimp plant (Barleria oenotheroides). AMERICAN JOURNAL OF BOTANY 2016; 103:1103-1116. [PMID: 27313197 DOI: 10.3732/ajb.1600083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/13/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Barleria is a large, pantropical genus of ca. 265 species mainly distributed in the Old World with only one species, B. oenotheroides, extending to the neotropics. This amphi-Atlantic disjunction, frequently displayed by pantropical taxa, has been traditionally explained with vicariance or geodispersal hypotheses and increasingly with long-distance dispersal. The native status of this species in the New World is controversial. METHODS A molecular phylogeographic study based on the nuclear ribosomal ITS region and plastid trnL-F, rps16, and trnS-G sequences was done to clarify the origin of this tropical intercontinental disjunction. Divergence times were estimated with various analytical approaches, including different markers and primary calibration points. KEY RESULTS Divergence ages estimated for Barleria lineages disagree with vicariance or geodispersal hypotheses. Genetic differentiation of American vs. African populations of B. oenotheroides does not support a recent anthropogenic introduction to the New World. Our data suggest ancient long-distance dispersal from the Old to the New World probably during the Pliocene or Upper Miocene. The number of dispersal events remains unclear. CONCLUSIONS Our study demonstrates the native status of Barleria in the New World, resolving one of only three presumed natural Old World-New World disjunctions at the species level among Acanthaceae. This case constitutes a further documented example of the "out-of-Africa" pattern in the family, despite their lack of documented assisted-dispersal syndromes, and highlights the importance of long-distance dispersal to explain pantropical distributions in many families.
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Affiliation(s)
- Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km 1, ES-41013, Seville, Spain Department of Botany, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, California 94118 USA
| | - Thomas F Daniel
- Department of Botany, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, California 94118 USA
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17
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Polle A, Chen S. On the salty side of life: molecular, physiological and anatomical adaptation and acclimation of trees to extreme habitats. PLANT, CELL & ENVIRONMENT 2015; 38:1794-816. [PMID: 25159181 DOI: 10.1111/pce.12440] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/11/2014] [Accepted: 08/17/2014] [Indexed: 05/04/2023]
Abstract
Saline and sodic soils that cannot be used for agriculture occur worldwide. Cultivating stress-tolerant trees to obtain biomass from salinized areas has been suggested. Various tree species of economic importance for fruit, fibre and timber production exhibit high salinity tolerance. Little is known about the mechanisms enabling tree crops to cope with high salinity for extended periods. Here, the molecular, physiological and anatomical adjustments underlying salt tolerance in glycophytic and halophytic model tree species, such as Populus euphratica in terrestrial habitats, and mangrove species along coastlines are reviewed. Key mechanisms that have been identified as mediating salt tolerance are discussed at scales from the genetic to the morphological level, including leaf succulence and structural adjustments of wood anatomy. The genetic and transcriptomic bases for physiological salt acclimation are salt sensing and signalling networks that activate target genes; the target genes keep reactive oxygen species under control, maintain the ion balance and restore water status. Evolutionary adaptation includes gene duplication in these pathways. Strategies for and limitations to tree improvement, particularly transgenic approaches for increasing salt tolerance by transforming trees with single and multiple candidate genes, are discussed.
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Affiliation(s)
- Andrea Polle
- Forstbotanik und Baumphysiologie, Büsgen-Institut, Georg-August Universität Göttingen, Göttingen, 37077, Germany
| | - Shaoliang Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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18
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Stölting KN, Paris M, Meier C, Heinze B, Castiglione S, Bartha D, Lexer C. Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree. THE NEW PHYTOLOGIST 2015; 207:723-34. [PMID: 25817433 DOI: 10.1111/nph.13392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/25/2015] [Indexed: 05/10/2023]
Abstract
Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic lineages of Populus alba (n = 48), thoroughly characterized by microsatellites (n = 317), and scanned their genomes for regions of unusually high allelic differentiation and reduced diversity using > 1.7 million single nucleotide polymorphisms (SNPs) from WGS. Results were confirmed by Sanger sequencing. On average, 9134 high-differentiation (≥ 4 standard deviations) outlier SNPs were uncovered between populations, 848 of which were shared by ≥ three replicate comparisons. Annotation revealed that 545 of these were located in 437 predicted genes. Twelve percent of differentiation outlier genome regions exhibited significantly reduced genetic diversity. Gene ontology (GO) searches were successful for 327 high-differentiation genes, and these were enriched for 63 GO terms. Our results provide a snapshot of the roles of 'hard selective sweeps' vs divergent selection of standing genetic variation in distinct postglacial recolonization lineages of P. alba. Thus, this study adds to our understanding of the mechanisms responsible for the origin of functionally relevant variation in temperate trees.
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Affiliation(s)
- Kai N Stölting
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland
| | - Margot Paris
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland
| | - Cécile Meier
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland
| | - Berthold Heinze
- Department of Forest Genetics, Austrian Research Centre for Forests (BFW), Seckendorff-Gudent Weg 8, 1130, Vienna, Austria
| | | | - Denes Bartha
- Department of Botany, West-Hungarian University, 9400, Sopron, Hungary
| | - Christian Lexer
- Unit of Ecology and Evolution, Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland
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Zhao P, Capella-Gutiérrez S, Shi Y, Zhao X, Chen G, Gabaldón T, Ma XF. Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation. BMC Genomics 2014; 15:872. [PMID: 25287394 PMCID: PMC4459065 DOI: 10.1186/1471-2164-15-872] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/29/2014] [Indexed: 12/22/2022] Open
Abstract
Background Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to
mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice
seeds have excellent nutrition value and have been historically consumed by local
populations in the desert regions of northwest China. Sand rice is a potential
food crop resilient to ongoing climate change; however, partly due to the scarcity
of genetic information, this species has undergone only little agronomic
modifications through classical breeding during recent years. Results We generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741
unigenes. Phylogenetic analysis based on 221 single-copy genes showed close
relationship between sand rice and the recently domesticated crop sugar beet.
Transcriptomic comparisons also showed a high level of global sequence
conservation between these two species. Conservation of sand rice and sugar beet
orthologs assigned to response to salt stress gene ontology term suggests that
sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far
more tolerant to high temperature. A set of genes likely relevant for resistance
to heat stress, was functionally annotated according to expression levels,
sequence annotation, and comparisons corresponding transcriptome profiling results
in Arabidopsis. Conclusions The present work provides abundant genomic information for functional dissection
of the important traits in sand rice. Future screening the genetic variation among
different ecotypes and constructing a draft genome sequence will further
facilitate agronomic trait improvement and final domestication of sand rice. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-872) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584, LT, Utrecht, The Netherlands.
| | - Yong Shi
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Xin Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Xiao-Fei Ma
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. .,Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
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