Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago
The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic...
Published in: | Molecular Phylogenetics and Evolution |
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Online Access: | http://hdl.handle.net/10261/334931 https://doi.org/10.1016/j.ympev.2023.107908 |
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ftcsic:oai:digital.csic.es:10261/334931 2024-02-11T10:03:19+01:00 Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago Jian, Jinjing Yuan, Yi Vilatersana, Roser Li, Linfeng Wang, Yuguo Zhang, Wenju Song, Zhiping Kong, Hongzhi Comes, Hans Peter Yang, Ji National Natural Science Foundation of China Science and Technology Commission of Shanghai Municipality 2023-08-18 http://hdl.handle.net/10261/334931 https://doi.org/10.1016/j.ympev.2023.107908 unknown Elsevier BV https://doi.org/10.1016/j.ympev.2023.107908 Sí doi:https://doi.org/10.1016/j.ympev.2023.107908 issn: 1055-7903 Molecular Phylogenetics and Evolution 188:107908(2023) http://hdl.handle.net/10261/334931 none Aegean archipelago Nigella Phylogenomics Population genomics Spatial–temporal evolution Speciation artículo 2023 ftcsic https://doi.org/10.1016/j.ympev.2023.107908 2024-01-16T11:52:48Z The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial¿temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a `mixing-isolation-mixing (MIM)" mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of "non-adaptive" radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales. This research was supported by the National Natural Science Foundation of China (Grant No. 91631308) and a grant from the Science and Technology Commission of Shanghai Municipality (14DZ2260400) 1. Introduction 2. Materials and methods 2.1. Taxon sampling 2.2. Transcriptome sequencing and de novo assembly 2.3. ... Article in Journal/Newspaper Day Island Digital.CSIC (Spanish National Research Council) Molecular Phylogenetics and Evolution 188 107908 |
institution |
Open Polar |
collection |
Digital.CSIC (Spanish National Research Council) |
op_collection_id |
ftcsic |
language |
unknown |
topic |
Aegean archipelago Nigella Phylogenomics Population genomics Spatial–temporal evolution Speciation |
spellingShingle |
Aegean archipelago Nigella Phylogenomics Population genomics Spatial–temporal evolution Speciation Jian, Jinjing Yuan, Yi Vilatersana, Roser Li, Linfeng Wang, Yuguo Zhang, Wenju Song, Zhiping Kong, Hongzhi Comes, Hans Peter Yang, Ji Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago |
topic_facet |
Aegean archipelago Nigella Phylogenomics Population genomics Spatial–temporal evolution Speciation |
description |
The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial¿temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a `mixing-isolation-mixing (MIM)" mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of "non-adaptive" radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales. This research was supported by the National Natural Science Foundation of China (Grant No. 91631308) and a grant from the Science and Technology Commission of Shanghai Municipality (14DZ2260400) 1. Introduction 2. Materials and methods 2.1. Taxon sampling 2.2. Transcriptome sequencing and de novo assembly 2.3. ... |
author2 |
National Natural Science Foundation of China Science and Technology Commission of Shanghai Municipality |
format |
Article in Journal/Newspaper |
author |
Jian, Jinjing Yuan, Yi Vilatersana, Roser Li, Linfeng Wang, Yuguo Zhang, Wenju Song, Zhiping Kong, Hongzhi Comes, Hans Peter Yang, Ji |
author_facet |
Jian, Jinjing Yuan, Yi Vilatersana, Roser Li, Linfeng Wang, Yuguo Zhang, Wenju Song, Zhiping Kong, Hongzhi Comes, Hans Peter Yang, Ji |
author_sort |
Jian, Jinjing |
title |
Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago |
title_short |
Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago |
title_full |
Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago |
title_fullStr |
Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago |
title_full_unstemmed |
Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago |
title_sort |
phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the nigella arvensis complex (ranunculaceae) in the aegean archipelago |
publisher |
Elsevier BV |
publishDate |
2023 |
url |
http://hdl.handle.net/10261/334931 https://doi.org/10.1016/j.ympev.2023.107908 |
genre |
Day Island |
genre_facet |
Day Island |
op_relation |
https://doi.org/10.1016/j.ympev.2023.107908 Sí doi:https://doi.org/10.1016/j.ympev.2023.107908 issn: 1055-7903 Molecular Phylogenetics and Evolution 188:107908(2023) http://hdl.handle.net/10261/334931 |
op_rights |
none |
op_doi |
https://doi.org/10.1016/j.ympev.2023.107908 |
container_title |
Molecular Phylogenetics and Evolution |
container_volume |
188 |
container_start_page |
107908 |
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1790599531549687808 |