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      Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China

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          Abstract

          Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes, whose members show strong geographic isolation in the mountains of southwest China. We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera, and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene. Widespread hybridization events were inferred within and between the identified clades and subclades. This suggests that hybridization occurred both early and late during diversification of subgenus Hymenanthes, although the extent to which hybridization, speciation through mixing-isolation-mixing or hybrid speciation, accelerated the diversification needs further exploration. Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species. Similar radiation processes may apply to other montane floras in this region and elsewhere.

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          The genomic substrate for adaptive radiation in African cichlid fish

          Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
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            Geological and climatic influences on mountain biodiversity

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              Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

              The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep-water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.
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                Author and article information

                Contributors
                Journal
                Natl Sci Rev
                Natl Sci Rev
                nsr
                National Science Review
                Oxford University Press
                2095-5138
                2053-714X
                December 2022
                02 December 2022
                02 December 2022
                : 9
                : 12
                : nwac276
                Affiliations
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University , Lanzhou 730000, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University , Cambridge, MA 02138, USA
                Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University , Wuhan 430079, China
                Royal Botanic Garden Edinburgh , Edinburgh EH3 5LR, UK
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University , Cambridge, MA 02138, USA
                State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University , Lanzhou 730000, China
                Negaunee Integrative Research Center , Field Museum, Chicago, IL 60605, USA
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                Royal Botanic Garden Edinburgh , Edinburgh EH3 5LR, UK
                Institute of Molecular Plant Sciences, The University of Edinburgh , Edinburgh EH9 3JH, UK
                Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University , Chengdu 610065, China
                State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University , Lanzhou 730000, China
                Author notes
                Corresponding author. E-mail: liujq@ 123456nwipb.cas.cn
                Corresponding author. E-mail: r.milne@ 123456ed.ac.uk
                Corresponding author. E-mail: huquanjun@ 123456scu.edu.cn

                Equally contributed to this work.

                Author information
                https://orcid.org/0000-0002-2955-6155
                https://orcid.org/0000-0002-7094-6868
                https://orcid.org/0000-0002-6866-5100
                https://orcid.org/0000-0002-2851-5474
                https://orcid.org/0000-0001-6922-2144
                https://orcid.org/0000-0002-4237-7418
                Article
                nwac276
                10.1093/nsr/nwac276
                9844246
                36687562
                667cc842-427b-4b7f-98d7-84c6bddd8876
                © The Author(s) 2022. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 July 2022
                : 29 November 2022
                : 30 November 2022
                : 17 January 2023
                Page count
                Pages: 11
                Funding
                Funded by: Chinese Academy of Sciences, DOI 10.13039/501100002367;
                Award ID: XDB31000000
                Funded by: National Natural Science Foundation of China, DOI 10.13039/501100001809;
                Award ID: 31590821
                Award ID: 91731301
                Funded by: National Key Research and Development Program of China, DOI 10.13039/501100012166;
                Award ID: 2017YFC0505203
                Funded by: Fundamental Research Funds for the Central Universities, DOI 10.13039/501100012226;
                Award ID: SCU2022D003
                Award ID: 2020SCUNL207
                Categories
                RESEARCH ARTICLE
                MOLECULAR BIOLOGY & GENETICS
                Special Topic: Species, Speciation and Biodiversity
                Nsr/8
                AcademicSubjects/MED00010
                AcademicSubjects/SCI00010

                evolutionary radiation,hybridization,rhododendron,subgenus hymenanthes,montane flora

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