Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data
The walnut family Juglandaceae was widely distributed in the Northern Hemisphere while several extant genera now exhibit intercontinental disjunctions. Recent progress in the systematics of Juglandaceae has greatly broadened our knowledge about its origin and evolution. However, there are still unce...
Published in: | Molecular Phylogenetics and Evolution |
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ACADEMIC PRESS INC ELSEVIER SCIENCE
2020
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Online Access: | http://ir.ibcas.ac.cn/handle/2S10CLM1/18162 https://doi.org/10.1016/j.ympev.2020.106802 |
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ftchiacadscibcas:oai:ir.ibcas.ac.cn:2S10CLM1/18162 2023-05-15T17:35:15+02:00 Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data Mu, Xian-Yun Tong, Ling Sun, Miao Zhu, Yi-Xuan Wen, Jun Lin, Qin-Wen Liu, Bing 2020 http://ir.ibcas.ac.cn/handle/2S10CLM1/18162 https://doi.org/10.1016/j.ympev.2020.106802 英语 eng ACADEMIC PRESS INC ELSEVIER SCIENCE MOLECULAR PHYLOGENETICS AND EVOLUTION http://ir.ibcas.ac.cn/handle/2S10CLM1/18162 doi:10.1016/j.ympev.2020.106802 cn.org.cspace.api.content.CopyrightPolicy@29e48b03 Juglandaceae RAD-Seq Chloroplast genome Divergence time Phylogenetic incongruence Juglans Biochemistry & Molecular Biology Evolutionary Biology Genetics & Heredity GENUS JUGLANS JUGLANDACEAE GENETIC DIVERSITY CHANGCHANG BASIN HAINAN ISLAND EOCENE HISTORY MORPHOLOGY DNA DIVERSIFICATION EVOLUTION Article 期刊论文 2020 ftchiacadscibcas https://doi.org/10.1016/j.ympev.2020.106802 2021-11-29T18:05:53Z The walnut family Juglandaceae was widely distributed in the Northern Hemisphere while several extant genera now exhibit intercontinental disjunctions. Recent progress in the systematics of Juglandaceae has greatly broadened our knowledge about its origin and evolution. However, there are still uncertainties about the intergeneric relationships within Juglandaceae, and discrepancies between fossil records and inferred divergence times for certain lineages were observed. In this study, well-resolved phylogenies of the Juglandaceae are reconstructed based on both the nuclear RAD-Seq and the whole chloroplast genome data. Our results support the Juglandoideae topology of (Hicoreae, (Platycaryeae, Juglandeae)) at the tribal level. Within Juglandeae, a discordant position of Pterocarya was detected between nuclear and plastid genome data, and a more likely topology (nuclear), (Juglans, (Pterocarya, Cyclocarya)), was discussed based on evidence from molecular data and fossil records. Based on carefully selected fossil calibrations, the divergence times of extant lineages were estimated and they corroborated well with fossil records (especially concerning Juglans and Pterocarya). Four sections within Juglans were strongly supported by the nuclear data. Within Juglans, the incongruent position of J. hopeiensis was recovered between the nuclear and plastid genomes. Yet the origin and evolutionary history of J. cinerea and J. hopeiensis are supported to be complicated and need further clarification. Integrative evidence from the fossil records, phylogeny and lineage divergence times shows that Juglandoideae originated in North America, and migrated to Eurasia via both the Bering and the North Atlantic land bridges. Our study shows the potential of integrative biogeographic studies for illuminating the evolutionary history of Juglandaceae. Article in Journal/Newspaper North Atlantic Institute of Botany: IBCAS OpenIR (Chinese Academy Of Sciences) Molecular Phylogenetics and Evolution 147 106802 |
institution |
Open Polar |
collection |
Institute of Botany: IBCAS OpenIR (Chinese Academy Of Sciences) |
op_collection_id |
ftchiacadscibcas |
language |
English |
topic |
Juglandaceae RAD-Seq Chloroplast genome Divergence time Phylogenetic incongruence Juglans Biochemistry & Molecular Biology Evolutionary Biology Genetics & Heredity GENUS JUGLANS JUGLANDACEAE GENETIC DIVERSITY CHANGCHANG BASIN HAINAN ISLAND EOCENE HISTORY MORPHOLOGY DNA DIVERSIFICATION EVOLUTION |
spellingShingle |
Juglandaceae RAD-Seq Chloroplast genome Divergence time Phylogenetic incongruence Juglans Biochemistry & Molecular Biology Evolutionary Biology Genetics & Heredity GENUS JUGLANS JUGLANDACEAE GENETIC DIVERSITY CHANGCHANG BASIN HAINAN ISLAND EOCENE HISTORY MORPHOLOGY DNA DIVERSIFICATION EVOLUTION Mu, Xian-Yun Tong, Ling Sun, Miao Zhu, Yi-Xuan Wen, Jun Lin, Qin-Wen Liu, Bing Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data |
topic_facet |
Juglandaceae RAD-Seq Chloroplast genome Divergence time Phylogenetic incongruence Juglans Biochemistry & Molecular Biology Evolutionary Biology Genetics & Heredity GENUS JUGLANS JUGLANDACEAE GENETIC DIVERSITY CHANGCHANG BASIN HAINAN ISLAND EOCENE HISTORY MORPHOLOGY DNA DIVERSIFICATION EVOLUTION |
description |
The walnut family Juglandaceae was widely distributed in the Northern Hemisphere while several extant genera now exhibit intercontinental disjunctions. Recent progress in the systematics of Juglandaceae has greatly broadened our knowledge about its origin and evolution. However, there are still uncertainties about the intergeneric relationships within Juglandaceae, and discrepancies between fossil records and inferred divergence times for certain lineages were observed. In this study, well-resolved phylogenies of the Juglandaceae are reconstructed based on both the nuclear RAD-Seq and the whole chloroplast genome data. Our results support the Juglandoideae topology of (Hicoreae, (Platycaryeae, Juglandeae)) at the tribal level. Within Juglandeae, a discordant position of Pterocarya was detected between nuclear and plastid genome data, and a more likely topology (nuclear), (Juglans, (Pterocarya, Cyclocarya)), was discussed based on evidence from molecular data and fossil records. Based on carefully selected fossil calibrations, the divergence times of extant lineages were estimated and they corroborated well with fossil records (especially concerning Juglans and Pterocarya). Four sections within Juglans were strongly supported by the nuclear data. Within Juglans, the incongruent position of J. hopeiensis was recovered between the nuclear and plastid genomes. Yet the origin and evolutionary history of J. cinerea and J. hopeiensis are supported to be complicated and need further clarification. Integrative evidence from the fossil records, phylogeny and lineage divergence times shows that Juglandoideae originated in North America, and migrated to Eurasia via both the Bering and the North Atlantic land bridges. Our study shows the potential of integrative biogeographic studies for illuminating the evolutionary history of Juglandaceae. |
format |
Article in Journal/Newspaper |
author |
Mu, Xian-Yun Tong, Ling Sun, Miao Zhu, Yi-Xuan Wen, Jun Lin, Qin-Wen Liu, Bing |
author_facet |
Mu, Xian-Yun Tong, Ling Sun, Miao Zhu, Yi-Xuan Wen, Jun Lin, Qin-Wen Liu, Bing |
author_sort |
Mu, Xian-Yun |
title |
Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data |
title_short |
Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data |
title_full |
Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data |
title_fullStr |
Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data |
title_full_unstemmed |
Phylogeny and divergence time estimation of the walnut family (Juglandaceae) based on nuclear RAD-Seq and chloroplast genome data |
title_sort |
phylogeny and divergence time estimation of the walnut family (juglandaceae) based on nuclear rad-seq and chloroplast genome data |
publisher |
ACADEMIC PRESS INC ELSEVIER SCIENCE |
publishDate |
2020 |
url |
http://ir.ibcas.ac.cn/handle/2S10CLM1/18162 https://doi.org/10.1016/j.ympev.2020.106802 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
MOLECULAR PHYLOGENETICS AND EVOLUTION http://ir.ibcas.ac.cn/handle/2S10CLM1/18162 doi:10.1016/j.ympev.2020.106802 |
op_rights |
cn.org.cspace.api.content.CopyrightPolicy@29e48b03 |
op_doi |
https://doi.org/10.1016/j.ympev.2020.106802 |
container_title |
Molecular Phylogenetics and Evolution |
container_volume |
147 |
container_start_page |
106802 |
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1766134355136086016 |