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Payne ARD, Mannion PD, Lloyd GT, Davis KE. Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs. Nat Ecol Evol 2024; 8:121-132. [PMID: 38049481 PMCID: PMC10781641 DOI: 10.1038/s41559-023-02244-0] [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: 06/17/2022] [Accepted: 09/26/2023] [Indexed: 12/06/2023]
Abstract
Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.
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Affiliation(s)
- Alexander R D Payne
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London, UK
| | | | - Katie E Davis
- Department of Biology, University of York, York, UK.
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2
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Zaharias P, Lemoine F, Gascuel O. Robustness of Felsenstein's Versus Transfer Bootstrap Supports With Respect to Taxon Sampling. Syst Biol 2023; 72:1280-1295. [PMID: 37756489 PMCID: PMC10939309 DOI: 10.1093/sysbio/syad052] [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: 02/24/2022] [Revised: 06/26/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein's bootstrap proportions (FBP) are the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tend to return low support for deep branches. The transfer bootstrap expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the binary {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports while inducing a very low number of falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with a high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depths, using empirical datasets. Our results show that the main critique of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.
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Affiliation(s)
- Paul Zaharias
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR7205–CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), 75005 Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Olivier Gascuel
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR7205–CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), 75005 Paris, France
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3
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Wang Y, Wang J, Chen Y, Liu S, Zhao Y, Chen N. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10024. [PMID: 36011659 PMCID: PMC9408514 DOI: 10.3390/ijerph191610024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
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Affiliation(s)
- Yichao Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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4
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Wang Y, Liu S, Wang J, Yao Y, Chen Y, Xu Q, Zhao Z, Chen N. Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:749982. [PMID: 35401648 PMCID: PMC8987724 DOI: 10.3389/fpls.2022.749982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000-200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be "super barcodes" for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.
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Affiliation(s)
- Yichao Wang
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shuya Liu
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jing Wang
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yanxin Yao
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yang Chen
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Planetary and Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qing Xu
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zengxia Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- Chinese Academy of Sciences Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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5
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Neubauer TA, Hauffe T, Silvestro D, Scotese CR, Stelbrink B, Albrecht C, Delicado D, Harzhauser M, Wilke T. Drivers of diversification in freshwater gastropods vary over deep time. Proc Biol Sci 2022; 289:20212057. [PMID: 35105242 PMCID: PMC8808086 DOI: 10.1098/rspb.2021.2057] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Unravelling the drivers of species diversification through geological time is of crucial importance for our understanding of long-term evolutionary processes. Numerous studies have proposed different sets of biotic and abiotic controls of speciation and extinction rates, but typically they were inferred for a single, long geological time frame. However, whether the impact of biotic and abiotic controls on diversification changes over time is poorly understood. Here, we use a large fossil dataset, a multivariate birth-death model and a comprehensive set of biotic and abiotic predictors, including a new index to quantify tectonic complexity, to estimate the drivers of diversification for European freshwater gastropods over the past 100 Myr. The effects of these factors on origination and extinction are estimated across the entire time frame as well as within sequential time windows of 20 Myr each. Our results find support for temporal heterogeneity in the factors associated with changes in diversification rates. While the factors impacting speciation and extinction rates vary considerably over time, diversity-dependence and topography are consistently important. Our study highlights that a high level of heterogeneity in diversification rates is best captured by incorporating time-varying effects of biotic and abiotic factors.
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Affiliation(s)
- Thomas A. Neubauer
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
- Marine Biodiversity, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
| | - Christopher R. Scotese
- Department of Earth and Planetary Sciences, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Björn Stelbrink
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Diana Delicado
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
| | - Mathias Harzhauser
- Geological-Paleontological Department, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring 26-32 (IFZ), 35392 Giessen, Germany
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6
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Xu Q, Cui Z, Chen N. Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time. Front Microbiol 2021; 12:742554. [PMID: 34803961 PMCID: PMC8597025 DOI: 10.3389/fmicb.2021.742554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
Chaetoceros is a species-rich diatom genus with broad distribution and plays an important role in global carbon cycle and aquatic ecosystems. However, genomic information of Chaetoceros species is limited, hindering advanced researches on Chaetoceros biodiversity and their differential impact on ecology. In this study, we constructed full-length chloroplast genomes (cpDNAs) for seven Chaetoceros species, including C. costatus, C. curvisetus, C. laevisporus, C. muelleri, C. pseudo-curvisetus, C. socialis, and C. tenuissimus. All of these cpDNAs displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The sizes of these cpDNAs were similar, ranging from 116,421 to 119,034 bp in size, and these cpDNAs also displayed similar GC content, ranging from 30.26 to 32.10%. Despite extensive synteny conservation, discrete regions showed high variations. Divergence time estimation revealed that the common ancestor of Chaetoceros species, which formed a monophyletic clade at approximately 58 million years ago (Mya), split from Acanthoceras zachariasii at about 70 Mya. The availability of cpDNAs of multiple Chaetoceros species provided valuable reference sequences for studying evolutionary relationship among Chaetoceros species, as well as between Chaetoceros species and other diatom species.
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Affiliation(s)
- Qing Xu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zongmei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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7
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Liu S, Wang Y, Xu Q, Zhang M, Chen N. Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation. BMC Genomics 2021; 22:746. [PMID: 34654361 PMCID: PMC8520197 DOI: 10.1186/s12864-021-07999-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Results In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya. Conclusions The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07999-z.
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Affiliation(s)
- Shuya Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yichao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Qing Xu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjia Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Nansheng Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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8
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Burki F, Sandin MM, Jamy M. Diversity and ecology of protists revealed by metabarcoding. Curr Biol 2021; 31:R1267-R1280. [PMID: 34637739 DOI: 10.1016/j.cub.2021.07.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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Affiliation(s)
- Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden; Science For Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
| | - Miguel M Sandin
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
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9
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Behrenfeld MJ, O'Malley R, Boss E, Karp-Boss L, Mundt C. Phytoplankton biodiversity and the inverted paradox. ISME COMMUNICATIONS 2021; 1:52. [PMID: 36750580 PMCID: PMC9723737 DOI: 10.1038/s43705-021-00056-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/08/2022]
Abstract
Earth's aquatic food webs are overwhelmingly supported by planktonic microalgae that live in the sunlit water column where only a minimum number of physical niches are readily identifiable. Despite this paucity of environmental differentiation, these "phytoplankton" populations exhibit a rich biodiversity, an observation not easily reconciled with broadly accepted rules of resource-based competitive exclusion. This conundrum is referred to as the "Paradox of the Plankton". Consideration of physical distancing between nutrient depletion zones around individual phytoplankton, however, suggests a competition-neutral resource landscape. Application of neutral theory to the sheer number of phytoplankton in physically-mixed water masses yields a prediction of astronomical biodiversity, suggesting the inverted paradox: Why are there so few phytoplankton species? Here, we introduce a trophic constraint on phytoplankton that, when combined with stochastic principals of ecological drift, predicts only modest levels of diversity in an otherwise competition-neutral landscape. Our "trophic exclusion" principle predicts diversity to be independent of population size and yields a species richness across cell-size classes that is consistent with broad oceanographic survey observations.
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Affiliation(s)
- Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
| | - Robert O'Malley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Christopher Mundt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
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10
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Abstract
Diatoms are a major primary producer in the modern oceans and play a critical role in the marine silica cycle. Their rise to dominance is recognized as one of the largest shifts in Cenozoic marine ecosystems, but the timing of this transition is debated. Here, we use a diagenetic model to examine the effect of sedimentation rate and temperature on the burial efficiency of biogenic silica over the past 66 million years (i.e., the Cenozoic). We find that the changing preservation potential of siliceous microfossils during that time would have overprinted the primary signal of diatom and radiolarian abundance. We generate a taphonomic null hypothesis of the diatom fossil record by assuming a constant flux of diatoms to the sea floor and having diagenetic conditions driven by observed shifts in temperature and sedimentation rate. This null hypothesis produces a late Cenozoic (∼5 Ma to 20 Ma) increase in the relative abundance of fossilized diatoms that is comparable to current empirical records. This suggests that the observed increase in diatom abundance in the sedimentary record may be driven by changing preservation potential. A late Cenozoic rise in diatoms has been causally tied to the rise of grasslands and baleen whales and to declining atmospheric CO2 levels. Here we suggest that the similarity among these records primarily arises from a common driver-the cooling climate system-that drove enhanced diatom preservation as well as the rise of grasslands and whales, rather than a causal link among them.
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11
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A Morpho-molecular Perspective on the Diversity and Evolution of Spumellaria (Radiolaria). Protist 2021; 172:125806. [PMID: 34174720 DOI: 10.1016/j.protis.2021.125806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
Spumellaria (Radiolaria, Rhizaria) are holoplanktonic amoeboid protists, ubiquitous and abundant in the global ocean. Their silicified skeleton preserves very well in sediments, displaying an excellent fossil record extremely valuable for paleo-environmental reconstruction studies, from where most of their extant diversity and ecology have been inferred. This study represents a comprehensive classification of Spumellaria based on the combination of ribosomal taxonomic marker genes (rDNA) and morphological characteristics. In contrast to established taxonomic knowledge, we demonstrate that symmetry of the skeleton takes more importance than internal structures at high classification ranks. Such reconsideration allows gathering different morphologies with concentric structure and spherical or radial symmetry believed to belong to other Radiolaria orders from the fossil record, as for some Entactinaria families. Our calibrated molecular clock dates the origin of Spumellaria in the middle Cambrian (ca. 515 Ma), among the first radiolarian representatives in the fossil record. This study allows a direct connection between living specimens and extinct morphologies from the Cambrian, bringing both a standpoint for future molecular environmental surveys and a better understanding for paleo-environmental reconstruction analysis.
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12
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Arribas P, Andújar C, Bidartondo MI, Bohmann K, Coissac É, Creer S, deWaard JR, Elbrecht V, Ficetola GF, Goberna M, Kennedy S, Krehenwinkel H, Leese F, Novotny V, Ronquist F, Yu DW, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Vogler AP, Papadopoulou A, Emerson BC. Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Mol Ecol 2021; 30:1120-1135. [PMID: 33432777 PMCID: PMC7986105 DOI: 10.1111/mec.15797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023]
Abstract
High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Carmelo Andújar
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Martin I. Bidartondo
- Department of Life SciencesImperial College LondonLondonUK
- Comparative Plant and Fungal BiologyRoyal Botanic GardensLondonUK
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Éric Coissac
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Jeremy R. deWaard
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphCanada
- School of Environmental SciencesUniversity of GuelphGuelphCanada
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM)Zoological Research Museum Alexander KoenigBonnGermany
| | - Gentile F. Ficetola
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
- Department of Environmental Sciences and PolicyUniversity of MilanoMilanoItaly
| | - Marta Goberna
- Department of Environment and AgronomyINIAMadridSpain
| | - Susan Kennedy
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Department of BiogeographyTrier UniversityTrierGermany
| | | | - Florian Leese
- Aquatic Ecosystem Research, Faculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU) EssenUniversity of Duisburg‐EssenEssenGermany
| | - Vojtech Novotny
- Biology Centre, Institute of EntomologyCzech Academy of SciencesCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Fredrik Ronquist
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Lucie Zinger
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | | | | | | | - Isaac Overcast
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
- Division of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkUSA
| | - Hélène Morlon
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Alfried P. Vogler
- Department of Life SciencesImperial College LondonLondonUK
- Department of Life SciencesNatural History MuseumLondonUK
| | | | - Brent C. Emerson
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
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13
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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14
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Cardoso GC, Abreu JM, Archer J, Crottini A, Mota PG. Independent evolution of song diversity and song motor performance in canaries, goldfinches and allies indicates clade-specific trade-offs in birdsong. Evolution 2020; 74:1170-1185. [PMID: 32352570 DOI: 10.1111/evo.13987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/12/2020] [Accepted: 04/26/2020] [Indexed: 11/29/2022]
Abstract
The diversity and the motor performance of birdsongs can both be sexually selected. In wood warblers, most species with high motor performance sing a greater proportion of trills, presumably to advertise performance, and thus have lower syllable diversity. We tested if this trade-off between motor performance and syllable diversity extends to canaries, goldfinches and allies, a clade with much longer and more varied songs. We assembled a molecular phylogeny and inferred song motor performance based on the speed of frequency modulation either in trills or in within-song intervals. The two metrics of performance were positively, but only mildly, related across species. While performance evaluated in intervals had high phylogenetic signal, performance evaluated in trills changed independently of phylogeny and was constrained by body size. Species in densely vegetated habitats sang fewer trills, but did not differ in motor performance. Contrary to wood warblers, song motor performance did not predict the proportion of trilled syllables nor within-song syllable diversity, perhaps because large differences in the song duration of canaries, goldfinches and allies prevent trills from severely compromising syllable diversity. Opposed results in wood warblers and in these finches indicate the existence of clade-specific trade-offs in the evolution of birdsong.
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Affiliation(s)
- Gonçalo C Cardoso
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal.,Behavioural Ecology Group, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark
| | - João M Abreu
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal
| | - John Archer
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal
| | - Angelica Crottini
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal
| | - Paulo G Mota
- CIBIO/InBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal.,Departamento de Ciências da Vida, Universidade de Coimbra, Coimbra, 3004-517, Portugal
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15
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Morlon H, Rolland J, Condamine FL. Response to technical comment 'A cautionary note for users of linear diversification dependencies'. Ecol Lett 2020; 23:1172-1174. [PMID: 32419323 DOI: 10.1111/ele.13513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/06/2020] [Accepted: 03/20/2020] [Indexed: 11/27/2022]
Abstract
The comment by Gamisch (2020) draws the attention of users of the R-package RPANDA (Methods Ecol. Evol., 7, 2016, 589) on situations when properly interpreting the results of linear diversification dependencies requires caution. Here we provide clarifications to help users interpreting their results when using any type of functional diversification dependencies with time or the environment.
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Affiliation(s)
- Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Jonathan Rolland
- Department of Zoology, University of British Columbia, University Blvd, #4200-6270, Vancouver, B.C, Canada.,Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015, Lausanne, Switzerland
| | - Fabien L Condamine
- Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier , Place Eugène Bataillon, 34095, Montpellier, France
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16
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Pinseel E, Janssens SB, Verleyen E, Vanormelingen P, Kohler TJ, Biersma EM, Sabbe K, Van de Vijver B, Vyverman W. Global radiation in a rare biosphere soil diatom. Nat Commun 2020; 11:2382. [PMID: 32404869 PMCID: PMC7221085 DOI: 10.1038/s41467-020-16181-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 04/20/2020] [Indexed: 11/09/2022] Open
Abstract
Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms. It is generally thought many microbes, owing to their ubiquity and dispersal capability, lack biogeographic structuring and clear speciation patterns compared to macroorganisms. However, Pinseel et al. demonstrate multiple cycles of colonization and diversification in Pinnularia borealis, a rare biosphere soil diatom.
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Affiliation(s)
- Eveline Pinseel
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium. .,Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium. .,Ecosystem Management Research Group (ECOBE), University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium. .,Department of Biological Sciences, University of Arkansas, 850 W Dickson St, SCEN 601, Fayetteville, AR, 72701-1201, USA.
| | | | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium.,Natuurpunt, Michiel Coxiestraat 11, 2800, Mechelen, Belgium
| | - Tyler J Kohler
- Department of Ecology, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic.,Stream Biofilm and Ecosystem Research Laboratory, École Polytechnique Fédérale Lausanne, GR B0 422, CH-1015, Lausanne, Switzerland
| | - Elisabeth M Biersma
- British Antarctic Survey, High Cross, Madingley Rd, Cambridge, CB3 0ET, UK.,Natural History Museum of Denmark, Øster Farimagsgade 5-Building 7, DK-1353, Copenhagen, Denmark
| | - Koen Sabbe
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Bart Van de Vijver
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.,Ecosystem Management Research Group (ECOBE), University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Wim Vyverman
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium.
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17
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Modica MV, Gorson J, Fedosov AE, Malcolm G, Terryn Y, Puillandre N, Holford M. Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification. Syst Biol 2020; 69:413-430. [PMID: 31504987 PMCID: PMC7164365 DOI: 10.1093/sysbio/syz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- UMR5247, Université de Montpellier CC 1703, Place Eugène Bataillon 34095 Montpellier, France
| | - Juliette Gorson
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
| | - Alexander E Fedosov
- Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, 33, Moscow 119071, Russia
| | - Gavin Malcolm
- Bird Hill, Barnes Lane, Milford on Sea, Hampshire, UK
| | - Yves Terryn
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
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18
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Billaud O, Moen DS, Parsons TL, Morlon H. Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past. Syst Biol 2020; 69:363-383. [PMID: 31682272 DOI: 10.1093/sysbio/syz057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 07/08/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023] Open
Abstract
Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.
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Affiliation(s)
- O Billaud
- Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France
| | - D S Moen
- Department of Integrative Biology, Oklahoma State University, 517 Life Sciences West, Stillwater, OK 74078, USA
| | - T L Parsons
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS UMR 8001, Paris, France
| | - H Morlon
- Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, École Normale Supérieure, Paris Sciences et Lettres (PSL) Research University, F-75005 Paris, France
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19
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Nakov T, Beaulieu JM, Alverson AJ. Diatoms diversify and turn over faster in freshwater than marine environments*. Evolution 2019; 73:2497-2511. [DOI: 10.1111/evo.13832] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/05/2019] [Accepted: 07/18/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Teofil Nakov
- Department of Biological Sciences University of Arkansas Fayetteville 1 University of Arkansas, SCEN 601 Fayetteville AR 72701
| | - Jeremy M. Beaulieu
- Department of Biological Sciences University of Arkansas Fayetteville 1 University of Arkansas, SCEN 601 Fayetteville AR 72701
| | - Andrew J. Alverson
- Department of Biological Sciences University of Arkansas Fayetteville 1 University of Arkansas, SCEN 601 Fayetteville AR 72701
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20
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Condamine FL, Rolland J, Morlon H. Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support. Ecol Lett 2019; 22:1900-1912. [DOI: 10.1111/ele.13382] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/20/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Fabien L. Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier Place Eugène Bataillon 34095Montpellier France
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
| | - Jonathan Rolland
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- Department of Computational Biology, Biophore University of Lausanne Lausanne 1015Switzerland
- Department of Zoology University of British Columbia University Blvd #4200‐6270Vancouver B.C Canada
| | - Hélène Morlon
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique) route de Saclay 91128Palaiseau France
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University F‐75005Paris France
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21
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Metabolic Innovations Underpinning the Origin and Diversification of the Diatom Chloroplast. Biomolecules 2019; 9:biom9080322. [PMID: 31366180 PMCID: PMC6723447 DOI: 10.3390/biom9080322] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022] Open
Abstract
Of all the eukaryotic algal groups, diatoms make the most substantial contributions to photosynthesis in the contemporary ocean. Understanding the biological innovations that have occurred in the diatom chloroplast may provide us with explanations to the ecological success of this lineage and clues as to how best to exploit the biology of these organisms for biotechnology. In this paper, we use multi-species transcriptome datasets to compare chloroplast metabolism pathways in diatoms to other algal lineages. We identify possible diatom-specific innovations in chloroplast metabolism, including the completion of tocopherol synthesis via a chloroplast-targeted tocopherol cyclase, a complete chloroplast ornithine cycle, and chloroplast-targeted proteins involved in iron acquisition and CO2 concentration not shared between diatoms and their closest relatives in the stramenopiles. We additionally present a detailed investigation of the chloroplast metabolism of the oil-producing diatom Fistulifera solaris, which is of industrial interest for biofuel production. These include modified amino acid and pyruvate hub metabolism that might enhance acetyl-coA production for chloroplast lipid biosynthesis and the presence of a chloroplast-localised squalene synthesis pathway unknown in other diatoms. Our data provides valuable insights into the biological adaptations underpinning an ecologically critical lineage, and how chloroplast metabolism can change even at a species level in extant algae.
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22
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Busseni G, Vieira FRJ, Amato A, Pelletier E, Pierella Karlusich JJ, Ferrante MI, Wincker P, Rogato A, Bowler C, Sanges R, Maiorano L, Chiurazzi M, d'Alcalà MR, Caputi L, Iudicone D. Meta-omics reveals genetic flexibility of diatom nitrogen transporters in response to environmental changes. Mol Biol Evol 2019; 36:2522-2535. [PMID: 31259367 PMCID: PMC6805229 DOI: 10.1093/molbev/msz157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/05/2019] [Accepted: 06/22/2019] [Indexed: 01/27/2023] Open
Abstract
Diatoms (Bacillariophyta), one of the most abundant and diverse groups of marine phytoplankton, respond rapidly to the supply of new nutrients, often out-competing other phytoplankton. Herein, we integrated analyses of the evolution, distribution and expression modulation of two gene families involved in diatom nitrogen uptake (DiAMT1 and DiNRT2), in order to infer the main drivers of divergence in a key functional trait of phytoplankton. Our results suggest that major steps in the evolution of the two gene families reflected key events triggering diatom radiation and diversification. Their expression is modulated in the contemporary ocean by seawater temperature, nitrate and iron concentrations. Moreover, the differences in diversity and expression of these gene families throughout the water column hint at a possible link with bacterial activity. This study represents a proof-of-concept of how a holistic approach may shed light on the functional biology of organisms in their natural environment.
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Affiliation(s)
- Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Fabio Rocha Jimenez Vieira
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CEA, INRA, CNRS. BIG, 17 rue des Martyrs Grenoble cedex 9, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,FR2022/Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
| | - Juan J Pierella Karlusich
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.,FR2022/Tara Oceans-GOSEE, 3 rue Michel-Ange, Paris, France
| | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, Italy
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, Trieste, Italy
| | - Luigi Maiorano
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma "La Sapienza", Viale dell'Università 32, Roma, Italy
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, Italy
| | | | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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Sandin MM, Pillet L, Biard T, Poirier C, Bigeard E, Romac S, Suzuki N, Not F. Time Calibrated Morpho-molecular Classification of Nassellaria (Radiolaria). Protist 2019; 170:187-208. [DOI: 10.1016/j.protis.2019.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/21/2019] [Accepted: 02/07/2019] [Indexed: 02/01/2023]
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