New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences
Subgenus Melanocrommyum is the second largest subgenus of Allium, with a wide distribution ranging from the Canary Islands to northwestern India. This study investigates the phylogeny, biogeographic patterns, and morphological character evolution of the subgenus using 117 accessions representing 107...
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| Format: | Article |
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KeAi Communications Co., Ltd.
2025-07-01
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| Series: | Plant Diversity |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265925000861 |
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| author | Ibrokhimjon Ergashov Ziyoviddin Yusupov Alireza Dolatyari Mina Khorasani İsmail Eker Nazgul Turdumatova Georgy Lazkov Farruhbek Rasulov Hang Sun Tao Deng Komiljon Tojibaev |
| author_facet | Ibrokhimjon Ergashov Ziyoviddin Yusupov Alireza Dolatyari Mina Khorasani İsmail Eker Nazgul Turdumatova Georgy Lazkov Farruhbek Rasulov Hang Sun Tao Deng Komiljon Tojibaev |
| author_sort | Ibrokhimjon Ergashov |
| collection | DOAJ |
| description | Subgenus Melanocrommyum is the second largest subgenus of Allium, with a wide distribution ranging from the Canary Islands to northwestern India. This study investigates the phylogeny, biogeographic patterns, and morphological character evolution of the subgenus using 117 accessions representing 107 taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum. Although the subgenus is monophyletic, significant incongruence exists between morphological and molecular data. Our plastome-based phylogenetic analysis identified five distinct lineages (A–E), corresponding to the geographic distributions of the species. However, plastome lineages (A–E) and ITS clusters (A–G) were incongruent. Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene. Our finding that Melanocrommyum plastomes have lost infA and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification. We also found that narrow leaves and fasciculate to semi-globose inflorescences may represent ancestral traits within the subgenus. This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum, suggesting recent diversification influenced by tectonic events and climate change, while highlighting the complexity of molecular and morphological data integration. |
| format | Article |
| id | doaj-art-6cd626a9e98f47c4a00a560a84bd0ad6 |
| institution | Kabale University |
| issn | 2468-2659 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj-art-6cd626a9e98f47c4a00a560a84bd0ad62025-08-20T03:25:55ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592025-07-0147456157510.1016/j.pld.2025.04.009New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequencesIbrokhimjon Ergashov0Ziyoviddin Yusupov1Alireza Dolatyari2Mina Khorasani3İsmail Eker4Nazgul Turdumatova5Georgy Lazkov6Farruhbek Rasulov7Hang Sun8Tao Deng9Komiljon Tojibaev10State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; University of Chinese Academy of Sciences, Beijing 100049, China; International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan; Flora of Uzbekistan Laboratory, Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan, 32 Durmon Yuli St., Tashkent 100125, Uzbekistan; Faculty of Natural Sciences, Fergana State University, Fergana 150100, UzbekistanState Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; International Joint Lab for Molecular Phylogeny and Biogeography, Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, UzbekistanPlant Bank, Iranian Biological Resource Center (IBRC), Iranian Academic Center for Education, Culture & Research (ACECR), Tehran, IranDepartment of Biology Education, Farhangian University, P.O. Box 14665_889, Tehran, IranBolu Abant İzzet Baysal University, Faculty of Science & Literature, Department of Biology, Bolu 14280, TürkiyeInstitute of Biology, National Academy of Sciences, Bishkek 720071, KyrgyzstanResearch Centre for Ecology and Environment of Central Asia, Bishkek 720040, KyrgyzstanAndijan State Medical Institute, Department of Pharmaceutical Sciences, Andijan, UzbekistanState Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Corresponding author. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Corresponding author.Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China; Flora of Uzbekistan Laboratory, Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan, 32 Durmon Yuli St., Tashkent 100125, Uzbekistan; Corresponding author. Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.Subgenus Melanocrommyum is the second largest subgenus of Allium, with a wide distribution ranging from the Canary Islands to northwestern India. This study investigates the phylogeny, biogeographic patterns, and morphological character evolution of the subgenus using 117 accessions representing 107 taxa across the 19 currently recognized sections within Allium subgenus Melanocrommyum. Although the subgenus is monophyletic, significant incongruence exists between morphological and molecular data. Our plastome-based phylogenetic analysis identified five distinct lineages (A–E), corresponding to the geographic distributions of the species. However, plastome lineages (A–E) and ITS clusters (A–G) were incongruent. Biogeographic and molecular dating analyses suggest that Melanocrommyum evolved in association with tectonic uplift events in Central Asia during the Late Miocene or Oligocene. Our finding that Melanocrommyum plastomes have lost infA and one copy rps19 gene indicate that the subgenus has undergone a relatively recent diversification. We also found that narrow leaves and fasciculate to semi-globose inflorescences may represent ancestral traits within the subgenus. This study provides new insights into the biogeographic history and trait evolution of Melanocrommyum, suggesting recent diversification influenced by tectonic events and climate change, while highlighting the complexity of molecular and morphological data integration.http://www.sciencedirect.com/science/article/pii/S2468265925000861BiogeographyComplete chloroplast genomeInfra-subgeneric groupingPhylogenyAlliumMelanocrommyum |
| spellingShingle | Ibrokhimjon Ergashov Ziyoviddin Yusupov Alireza Dolatyari Mina Khorasani İsmail Eker Nazgul Turdumatova Georgy Lazkov Farruhbek Rasulov Hang Sun Tao Deng Komiljon Tojibaev New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences Plant Diversity Biogeography Complete chloroplast genome Infra-subgeneric grouping Phylogeny Allium Melanocrommyum |
| title | New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences |
| title_full | New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences |
| title_fullStr | New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences |
| title_full_unstemmed | New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences |
| title_short | New insights into the molecular phylogeny and biogeographical history of Allium subgenus Melanocrommyum (Amaryllidaceae) based on plastome and nuclear sequences |
| title_sort | new insights into the molecular phylogeny and biogeographical history of allium subgenus melanocrommyum amaryllidaceae based on plastome and nuclear sequences |
| topic | Biogeography Complete chloroplast genome Infra-subgeneric grouping Phylogeny Allium Melanocrommyum |
| url | http://www.sciencedirect.com/science/article/pii/S2468265925000861 |
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