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Gutiérrez-Larruscain D, Vargas P, Fernández-Mazuecos M, Pausas JG. Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers. Mol Phylogenet Evol 2024; 199:108162. [PMID: 39067655 DOI: 10.1016/j.ympev.2024.108162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/10/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.
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Affiliation(s)
- David Gutiérrez-Larruscain
- Department of Ecology and Global Change, Desertification Research Centre (CIDE: CSIC-UV-GVA), Valencia, Spain.
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB: CSIC), Madrid, Spain
| | - Mario Fernández-Mazuecos
- Department of Biology (Botany), Faculty of Sciences, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Juli G Pausas
- Department of Ecology and Global Change, Desertification Research Centre (CIDE: CSIC-UV-GVA), Valencia, Spain
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2
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Cui X, Liu K, Li E, Zhang Z, Dong W. Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species. Int J Mol Sci 2024; 25:6786. [PMID: 38928490 PMCID: PMC11203854 DOI: 10.3390/ijms25126786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. Caragana species are ecologically valuable for their roles in windbreaking and sand fixation. However, the taxonomy and phylogenetic relationships of the genus Caragana are still unclear. In this study, we sequenced and assembled the chloroplast genomes of representative species of Caragana and reconstructed robust phylogenetic relationships at the section level. The Caragana chloroplast genome has lost the inverted repeat region and wascategorized in the inverted repeat loss clade (IRLC). The chloroplast genomes of the eight species ranged from 128,458 bp to 135,401 bp and contained 110 unique genes. All the Caragana chloroplast genomes have a highly conserved structure and gene order. The number of long repeats and simple sequence repeats (SSRs) showed significant variation among the eight species, indicating heterogeneous evolution in Caragana. Selective pressure analysis of the genes revealed that most of the protein-coding genes evolved under purifying selection. The phylogenetic analyses indicated that each section forms a clade, except the section Spinosae, which was divided into two clades. This study elucidated the evolution of the chloroplast genome within the widely distributed genus Caragana. The detailed information obtained from this study can serve as a valuable resource for understanding the molecular dynamics and phylogenetic relationships within Caragana.
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Affiliation(s)
| | | | | | - Zhixiang Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.C.); (K.L.); (E.L.)
| | - Wenpan Dong
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; (X.C.); (K.L.); (E.L.)
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3
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Wang Q, Chen X, Meng Y, Niu M, Jia Y, Huang L, Ma W, Liang C, Li Z, Zhao L, Dang Z. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. Int J Mol Sci 2024; 25:2084. [PMID: 38396759 PMCID: PMC10888960 DOI: 10.3390/ijms25042084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Caragana, a xerophytic shrub genus widely distributed in northern China, exhibits distinctive geographical substitution patterns and ecological adaptation diversity. This study employed transcriptome sequencing technology to investigate 12 Caragana species, aiming to explore genic-SSR variations in the Caragana transcriptome and identify their role as a driving force for environmental adaptation within the genus. A total of 3666 polymorphic genic-SSRs were identified across different species. The impact of these variations on the expression of related genes was analyzed, revealing a significant linear correlation (p < 0.05) between the length variation of 264 polymorphic genic-SSRs and the expression of associated genes. Additionally, 2424 polymorphic genic-SSRs were located in differentially expressed genes among Caragana species. Through weighted gene co-expression network analysis, the expressions of these genes were correlated with 19 climatic factors and 16 plant functional traits in various habitats. This approach facilitated the identification of biological processes associated with habitat adaptations in the studied Caragana species. Fifty-five core genes related to functional traits and climatic factors were identified, including various transcription factors such as MYB, TCP, ARF, and structural proteins like HSP90, elongation factor TS, and HECT. The roles of these genes in the ecological adaptation diversity of Caragana were discussed. Our study identified specific genomic components and genes in Caragana plants responsive to heterogeneous habitats. The results contribute to advancements in the molecular understanding of their ecological adaptation, lay a foundation for the conservation and development of Caragana germplasm resources, and provide a scientific basis for plant adaptation to global climate change.
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Affiliation(s)
- Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Xing’er Chen
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yue Meng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Yuanyuan Jia
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Lei Huang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Wenhong Ma
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Cunzhu Liang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhiyong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Liqing Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
| | - Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Q.W.); (X.C.); (Y.M.); (M.N.); (Y.J.); (L.H.); (W.M.); (C.L.); (Z.L.); (L.Z.)
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Inner Mongolia Autonomous Region, Hohhot 010021, China
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Chen YP, Turdimatovich TO, Nuraliev MS, Lazarević P, Drew BT, Xiang CL. Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae). Cladistics 2022; 38:429-451. [PMID: 35358338 DOI: 10.1111/cla.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/28/2022] Open
Abstract
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Maxim S Nuraliev
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Predrag Lazarević
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, 68849, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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5
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Othman SN, Litvinchuk SN, Maslova I, Dahn H, Messenger KR, Andersen D, Jowers MJ, Kojima Y, Skorinov DV, Yasumiba K, Chuang MF, Chen YH, Bae Y, Hoti J, Jang Y, Borzee A. From Gondwana to the Yellow Sea, evolutionary diversifications of true toads Bufo sp. in the Eastern Palearctic and a revisit of species boundaries for Asian lineages. eLife 2022; 11:e70494. [PMID: 35089130 PMCID: PMC8920510 DOI: 10.7554/elife.70494] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Taxa with vast distribution ranges often display unresolved phylogeographic structures and unclear taxonomic boundaries resulting in hidden diversity. This hypothesis-driven study reveals the evolutionary history of Bufonidae, covering the phylogeographic patterns found in Holarctic bufonids from the West Gondwana to the phylogenetic taxonomy of Asiatic true toads in the Eastern Palearctic. We used an integrative approach relying on fossilized birth-death calibrations, population dynamics, gene-flow, species distribution, and species delimitation modeling to resolve the biogeography of the clade and highlight cryptic lineages. We verified the near-simultaneous Miocene radiations within Western and Eastern Palearctic Bufo, c. 14.49-10.00 Mya, temporally matching with the maximum dust outflows in Central Asian deserts. Contrary to earlier studies, we demonstrated that the combined impacts of long dispersal and ice-age refugia equally contributed to the current genetic structure of Bufo in East Asia. Our findings reveal a climate-driven adaptation in septentrional Eastern Asian Bufo, explaining its range shifts toward northern latitudes. We resolve species boundaries within the Eastern Palearctic Bufo, and redefine the taxonomic and conservation units of the northeastern species: B. sachalinensis and its subspecies.
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Affiliation(s)
- Siti N Othman
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
- Department of Life Sciences and Division of EcoScience, Ewha Womans UniversitySeoulRepublic of Korea
| | - Spartak N Litvinchuk
- Institute of Cytology, Russian Academy of SciencesSt. PetersburgRussian Federation
| | - Irina Maslova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of SciencesVladivostokRussian Federation
| | - Hollis Dahn
- Department of Ecology and Evolutionary Biology, University of TorontoTorontoCanada
| | - Kevin R Messenger
- Herpetology and Applied Conservation Laboratory, College of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
| | - Desiree Andersen
- Department of Life Sciences and Division of EcoScience, Ewha Womans UniversitySeoulRepublic of Korea
| | - Michael J Jowers
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do PortoVairãoPortugal
| | - Yosuke Kojima
- Graduate School of Human and Environmental Studies, Kyoto UniversityKyotoJapan
| | - Dmitry V Skorinov
- Institute of Cytology, Russian Academy of SciencesSt. PetersburgRussian Federation
| | | | - Ming-Feng Chuang
- Department of Life Sciences and Research Center for Global Change Biology, National Chung Hsing UniversityTaichungTaiwan
| | - Yi-Huey Chen
- Department of Life Science, Chinese Culture UniversityTaipeiTaiwan
| | - Yoonhyuk Bae
- Department of Life Sciences and Division of EcoScience, Ewha Womans UniversitySeoulRepublic of Korea
| | - Jennifer Hoti
- Department of Life Sciences and Division of EcoScience, Ewha Womans UniversitySeoulRepublic of Korea
- Department of Life Sciences and Systems Biology, University of TurinTurinItaly
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans UniversitySeoulRepublic of Korea
| | - Amael Borzee
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry UniversityNanjingChina
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Genetic Diversity Analysis and Potential Distribution Prediction of Sophora moorcroftiana Endemic to Qinghai–Tibet Plateau, China. FORESTS 2021. [DOI: 10.3390/f12081106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sophora moorcroftiana (Benth.) Baker is an endemic woody species distributed in the Qinghai–Tibet Plateau (QTP), a part of the world characterized by high altitude and cold weather. In this study, the genetic diversity of S. moorcroftiana was evaluated based on 300 representative samples of 15 populations using 20 polymorphic SSR markers, and its potential distribution was predicted according to 19 bioclimatic factors using MaxEnt modeling. Results showed the population genetic diversity of S. moorcroftiana was generally not high (around 0.5), and the range of variation was small (0.437–0.539). Altitude, rather than other environmental factors, was the key factor affecting the present genetic diversity. Moreover, due to climate change in the QTP, the suitable area is increasing and will continue to increase by 48.35%, 84.44%, 101.98%, and 107.30% in the four future periods of 2030s, 2050s, 2070s, and 2090s, respectively, compared to the present, which is beneficial for S. moorcroftiana. These results will provide a theoretical basis for the development of germplasm conservation strategies for S. moorcroftiana and enrich information on the impacts of climate change on plants in the QTP.
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Barbolini N, Woutersen A, Dupont-Nivet G, Silvestro D, Tardif D, Coster PMC, Meijer N, Chang C, Zhang HX, Licht A, Rydin C, Koutsodendris A, Han F, Rohrmann A, Liu XJ, Zhang Y, Donnadieu Y, Fluteau F, Ladant JB, Le Hir G, Hoorn C. Cenozoic evolution of the steppe-desert biome in Central Asia. SCIENCE ADVANCES 2020; 6:eabb8227. [PMID: 33036969 PMCID: PMC7546705 DOI: 10.1126/sciadv.abb8227] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/20/2020] [Indexed: 05/26/2023]
Abstract
The origins and development of the arid and highly seasonal steppe-desert biome in Central Asia, the largest of its kind in the world, remain largely unconstrained by existing records. It is unclear how Cenozoic climatic, geological, and biological forces, acting at diverse spatial and temporal scales, shaped Central Asian ecosystems through time. Our synthesis shows that the Central Asian steppe-desert has existed since at least Eocene times but experienced no less than two regime shifts, one at the Eocene-Oligocene Transition and one in the mid-Miocene. These shifts separated three successive "stable states," each characterized by unique floral and faunal structures. Past responses to disturbance in the Asian steppe-desert imply that modern ecosystems are unlikely to recover their present structures and diversity if forced into a new regime. This is of concern for Asian steppes today, which are being modified for human use and lost to desertification at unprecedented rates.
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Affiliation(s)
- N Barbolini
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, Netherlands.
- Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - A Woutersen
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, Netherlands.
| | - G Dupont-Nivet
- Universität Potsdam, Institute of Geosciences, 14476 Potsdam, Germany
- Université de Rennes, CNRS, Géosciences Rennes-UMR 6118, F-35000 Rennes, France
- Key Laboratory of Orogenic Belts and Crustal Evolution, Peking University, Beijing 100871, China
| | - D Silvestro
- Department of Biology, University of Fribourg, Ch. De Musée 10, Fribourg, Switzerland
| | - D Tardif
- Institut de Physique du Globe, Paris 75005, France
| | - P M C Coster
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - N Meijer
- Universität Potsdam, Institute of Geosciences, 14476 Potsdam, Germany
| | - C Chang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - H-X Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - A Licht
- Department of Earth and Space Sciences, University of Washington, Seattle, WA 98195, USA
| | - C Rydin
- Department of Ecology, Environment and Plant Sciences and Bolin Centre for Climate Research, Stockholm University, SE-106 91 Stockholm, Sweden
- The Bergius Foundation, The Royal Swedish Academy of Sciences, Box 50005, SE-104 05 Stockholm, Sweden
| | - A Koutsodendris
- Institute of Earth Sciences, Heidelberg University, Heidelberg 69120, Germany
| | - F Han
- School of Earth Sciences, East China University of Technology, Nanchang 330013, Jiangxi, China
| | - A Rohrmann
- Universität Potsdam, Institute of Geosciences, 14476 Potsdam, Germany
| | - X-J Liu
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
| | - Y Zhang
- The First Monitoring and Application Center, China Earthquake Administration, Tianjin 300180, China
| | - Y Donnadieu
- Laboratoire des Sciences du Climat et de l'Environnement (LSCE)/Institute Pierre Simon Laplace (IPSL), Commissariat á l'Énergie Atomique et aux Énergies Alternatives (CEA)-CNRS-Université de Versailles Saint Quentin-en-Yvelines (UVSQ), Université Paris-Saclay, Gif-sur-Yvette, France
- Aix-Marseille Université, CNRS, Institut pour la Recherche et le Développement (IRD), Collège de France, Centre de Recherche et d'Enseignement de Géosciences de l'Environnement (CEREGE), Aix-en-Provence, France
| | - F Fluteau
- Institut de Physique du Globe, Paris 75005, France
| | - J-B Ladant
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - G Le Hir
- Institut de Physique du Globe, Paris 75005, France
| | - C Hoorn
- Department of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, Netherlands.
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Hrivniak Ľ, Sroka P, Bojková J, Godunko RJ, Soldán T, Staniczek AH. The impact of Miocene orogeny for the diversification of Caucasian Epeorus (Caucasiron) mayflies (Ephemeroptera: Heptageniidae). Mol Phylogenet Evol 2020; 146:106735. [PMID: 32001364 DOI: 10.1016/j.ympev.2020.106735] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/26/2022]
Abstract
A common hypothesis for the high biodiversity of mountains is the diversification driven by orogeny creating conditions for rapid in situ speciation of resident lineages. The Caucasus is a young mountain system considered as a biodiversity hotspot; however, the origin and evolution of its diversity remain poorly understood. This study focuses on mayflies of the subgenus Caucasiron, one of the most diversified stenotopic mayflies inhabiting various types of streams throughout the Caucasus. Using the time-calibrated phylogeny based on two mitochondrial (COI, 16S) and three nuclear (EF-1α, wg, 28S) gene fragments, we tested the role of Caucasian orogeny in biogeography, diversification patterns, and altitudinal diversification of Caucasiron mayflies. We found that orogeny promoted the lineage diversification of Caucasiron in the Miocene. The highest diversification rate corresponding with the uplift of mountains was followed by a significant slowdown towards the present suggesting minor influence of Pleistocene climatic oscillations on the speciation. The Caucasiron lineages cluster into three principal clades originating in the Upper Miocene. We found a strong support that one of the three clades diversified via allopatric speciation in the Greater Caucasus isolated in the Parathetys Sea. The other two clades originating most likely outside the Greater Caucasus diversified towards high and low altitude, respectively, indicating possible role of climatic factors and/or passive uplift on their differentiation. Current high Caucasiron diversity in the Greater Caucasus is a result of in situ speciation and later immigration from adjacent mountain ranges after the Parathetys Sea retreat. Our phylogeny supported the monophyly of Rhithrogeninae, Epeorus s.l., Caucasiron, and Iron. Epeorus subgenus Ironopsis was found paraphyletic, with its European representatives more closely related to Epeorus s.str. than to Iron. Therefore, we re-arranged taxa treated within Ironopsis to comply with the phylogeny recovered herein.
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Affiliation(s)
- Ľuboš Hrivniak
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic; Faculty of Sciences, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Pavel Sroka
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jindřiška Bojková
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman J Godunko
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic; Department of Invertebrate Zoology and Hydrobiology, University of Łódź, Banacha 12/16, 90237 Łódź, Poland
| | - Tomáš Soldán
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Arnold H Staniczek
- Department of Entomology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
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Evolutionary history of the Pasque-flowers (Pulsatilla, Ranunculaceae): Molecular phylogenetics, systematics and rDNA evolution. Mol Phylogenet Evol 2019; 135:45-61. [PMID: 30831271 DOI: 10.1016/j.ympev.2019.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/25/2019] [Accepted: 02/17/2019] [Indexed: 11/23/2022]
Abstract
Pulsatilla (Anemoneae, Ranunculaceae) is sister to Anemone s.s. and contains ca 40 perennial species of considerable horticultural and medical importance. We sequenced 31 of those species, plus nine subspecies, two cultivars and six outgroups, for two nuclear regions (high-copy nrITS and low-copy MLH1) and three plastid regions (rbcL, accD-psaI, trnL intron) in order to generate the first comprehensive species-level phylogeny of the genus. Phylogenetic trees were constructed using both concatenation-based (maximum likelihood and Bayesian inference) and coalescence methods. The better supported among the internal nodes were subjected to molecular clock dating and ancestral area reconstruction, and karyotypic characters identified by us using Fluorescence In Situ Hybridization were mapped across the tree. The preferred species tree from the coalescence analysis formed the basis of a new infrageneric classification based on monophyly plus degree of divergence. The earliest divergent of the three subgenera, Kostyczewianae, is represented by only a single species that is morphologically intermediate between Anemone s.s. and 'core' Pulsatilla. Subgenus Pulsatilla is considerably richer in species than its sister subgenus Preonanthus and contains three monophyletic sections. Species possessing nodding flowers and pectinately dissected leaves are phylogenetically derived compared with groups possessing erect flowers and palmately lobed leaves. Pulsatilla separated from Anemone s.s. at ca 25 Ma. Our results indicate a central Asian mountain origin of the genus and an initial diversification correlated with late Tertiary global cooling plus regional mountain uplift, aridification and consequent expansion of grasslands. The more rapid and extensive diversification within subgenus Pulsatilla began at ca 3 Ma and continued throughout the Quaternary, driven not only by major perturbations in global climate but also by well-documented polyploidy.
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10
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Li M, Xie D, Xie C, Deng Y, Zhong Y, Yu Y, He X. A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Alliums (Amaryllidaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:149. [PMID: 30891047 PMCID: PMC6412145 DOI: 10.3389/fpls.2019.00149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/28/2019] [Indexed: 05/20/2023]
Abstract
The Qinghai-Tibet Plateau (QTP) has been biogeographically divided into the eastern monsoonal and the western continental climatic zones along the 500 mm isohyet. However, this biogeographic hypothesis has been rarely tested using a phylogeographic approach. The members of the genus Allium subgenus Cyathophora coincidentally distribute across this biogeographical divide. Intriguingly, Allium fasciculatum of subgenus Amerallium co-occurs in the distribution range of subgenus Cyathophora. To illuminate the role of this biogeographic divide on the genetic divergence, we genotyped 466 individuals of 52 populations of subgenus Cyathophora and 110 individuals of 19 populations of A. fasciculatum using three chloroplast DNA fragments, whole nrITS and nine nuclear microsatellite loci, supplemented with the present environmental space and paleo-distribution modeling. Our phylogeographical evidence recovered the concordant east-west genetic breaks both for subgenus Cyathophora and A. fasciculatum along the 500 mm isohyet. The divergence time estimations and environmental niche differentiations suggested this east-west genetic breaks could have been triggered by the climatic-induced vicariance during the early Pleistocene. Noticeably, this split within subgenus Cyathophora could have been deepened by the morphological vicariance from the eastern umbel to the western spicate, while that within A. fasciculatum could have been obscured due to the pollen flows from the east to west caused by the postglacial expansion. The genetic structures and ecological niche modelings (ENMs) recovered the distinct responses to the Quaternary climatic oscillations for species constricted to different climatic zones, further highlighting the profound effect of the climatic differences and tectonic uplifts on the genetic diversification. Overall, our findings offer strong evidence for the existence of a biogeographic divide between the eastern monsoonal and the west continental climatic zones of the QTP nearly along the 500 mm isohyet.
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Seed germination of Caragana species from different regions is strongly driven by environmental cues and not phylogenetic signals. Sci Rep 2017; 7:11248. [PMID: 28900140 PMCID: PMC5596004 DOI: 10.1038/s41598-017-11294-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022] Open
Abstract
Seed germination behavior is an important factor in the distribution of species. Many studies have shown that germination is controlled by phylogenetic constraints, however, it is not clear whether phylogenetic constraints or environmental cues explain seed germination of a genus from a common ancestor. In this study, seed germination under different temperature- and water-regimes [induced by different osmotic potentials of polyethylene glycol (PEG)] was investigated in the phylogenetically-related Caragana species that thrive in arid, semiarid, semihumid and humid environments. The results showed that the final percentage germination (FPG) decreased from 95% in species from arid habitats to 0% in species from humid habitats, but with no significant phylogenetic signal. Rather, the response of seed germination to temperature and PEG varied greatly with species from arid to humid habitats and was tightly linked to the ecological niche of the species, their seed coat structure and abscisic acid concentration. The findings are not consistent with the hypothesis that within a family or a genus, seed germination strategies can be a stable evolutionary trait, thus constraining interspecific variation, but the results clearly show that seed germination of Caragana species distributed across a range of habitats has adapted to the environment of that habitat.
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