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Madeira P, Reddy MM, Assis J, Bolton JJ, Rothman MD, Anderson RJ, Kandjengo L, Kreiner A, Coleman MA, Wernberg T, De Clerck O, Leliaert F, Bandeira S, Ada AM, Neiva J, Pearson GA, Serrão EA. Cryptic diversity in southern African kelp. Sci Rep 2024; 14:11071. [PMID: 38745036 PMCID: PMC11093989 DOI: 10.1038/s41598-024-61336-4] [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: 07/31/2023] [Accepted: 05/04/2024] [Indexed: 05/16/2024] Open
Abstract
The southern coast of Africa is one of the few places in the world where water temperatures are predicted to cool in the future. This endemism-rich coastline is home to two sister species of kelps of the genus Ecklonia maxima and Ecklonia radiata, each associated with specific thermal niches, and occuring primarily on opposite sides of the southern tip of Africa. Historical distribution records indicate that E. maxima has recently shifted its distribution ~ 70 km eastward, to sites where only E. radiata was previously reported. The contact of sister species with contrasting thermal affinities and the occurrence of mixed morphologies raised the hypothesis that hybridization might be occurring in this contact zone. Here we describe the genetic structure of the genus Ecklonia along the southern coast of Africa and investigate potential hybridization and cryptic diversity using a combination of nuclear microsatellites and mitochondrial markers. We found that both species have geographically discrete genetic clusters, consistent with expected phylogeographic breaks along this coastline. In addition, depth-isolated populations were found to harbor unique genetic diversity, including a third Ecklonia lineage. Mito-nuclear discordance and high genetic divergence in the contact zones suggest multiple hybridization events between Ecklonia species. Discordance between morphological and molecular identification suggests the potential influence of abiotic factors leading to convergent phenotypes in the contact zones. Our results highlight an example of cryptic diversity and hybridization driven by contact between two closely related keystone species with contrasting thermal affinities.
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Affiliation(s)
- Pedro Madeira
- CCMAR, University of Algarve, Gambelas, Faro, Portugal.
| | - Maggie M Reddy
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa.
| | - Jorge Assis
- CCMAR, University of Algarve, Gambelas, Faro, Portugal
- Faculty of Bioscience and Aquaculture, Nord Universitet, Bodø, Norway
| | - John J Bolton
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa.
| | - Mark D Rothman
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa.
- Department of Environment, Forestry and Fisheries, Private Bag X2, Vlaeberg, 8012, South Africa.
| | - Robert J Anderson
- Department of Biological Sciences, University of Cape Town, Cape Town, 7701, South Africa
| | - Lineekela Kandjengo
- Department of Fisheries and Ocean Sciences, University of Namibia, Sam Nujoma Campus, Henties Bay, Namibia
| | - Anja Kreiner
- National Marine Information and Research Centre, Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | - Melinda A Coleman
- New South Wales Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
- National Marine Science Centre, Southern Cross University, 2 Bay Drive, Coffs Harbour, NSW, 2450, Australia
- UWA Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Thomas Wernberg
- UWA Oceans Institute and School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Olivier De Clerck
- Biology Department, Ghent University, Krijgslaan 281 S8, 9000, Ghent, Belgium
| | | | - Salomão Bandeira
- Department of Biological Sciences, Eduardo Mondlane University, Maputo, Mozambique
| | - Abdul M Ada
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - João Neiva
- CCMAR, University of Algarve, Gambelas, Faro, Portugal
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De Saeger J, Coulembier Vandelannoote E, Lee H, Park J, Blomme J. Genome editing in macroalgae: advances and challenges. Front Genome Ed 2024; 6:1380682. [PMID: 38516199 PMCID: PMC10955705 DOI: 10.3389/fgeed.2024.1380682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
This minireview examines the current state and challenges of genome editing in macroalgae. Despite the ecological and economic significance of this group of organisms, genome editing has seen limited applications. While CRISPR functionality has been established in two brown (Ectocarpus species 7 and Saccharina japonica) and one green seaweed (Ulva prolifera), these studies are limited to proof-of-concept demonstrations. All studies also (co)-targeted ADENINE PHOSPHORIBOSYL TRANSFERASE to enrich for mutants, due to the relatively low editing efficiencies. To advance the field, there should be a focus on advancing auxiliary technologies, particularly stable transformation, so that novel editing reagents can be screened for their efficiency. More work is also needed on understanding DNA repair in these organisms, as this is tightly linked with the editing outcomes. Developing efficient genome editing tools for macroalgae will unlock the ability to characterize their genes, which is largely uncharted terrain. Moreover, given their economic importance, genome editing will also impact breeding campaigns to develop strains that have better yields, produce more commercially valuable compounds, and show improved resilience to the impacts of global change.
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Affiliation(s)
- Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Emma Coulembier Vandelannoote
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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Cock JM. The model system Ectocarpus: Integrating functional genomics into brown algal research. JOURNAL OF PHYCOLOGY 2023; 59:4-8. [PMID: 36477437 DOI: 10.1111/jpy.13310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Affiliation(s)
- J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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Bringloe TT, Fort A, Inaba M, Sulpice R, Ghriofa CN, Mols‐Mortensen A, Filbee‐Dexter K, Vieira C, Kawai H, Hanyuda T, Krause‐Jensen D, Olesen B, Starko S, Verbruggen H. Whole genome population structure of North Atlantic kelp confirms high-latitude glacial refugia. Mol Ecol 2022; 31:6473-6488. [PMID: 36200326 PMCID: PMC10091776 DOI: 10.1111/mec.16714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Coastal refugia during the Last Glacial Maximum (~21,000 years ago) have been hypothesized at high latitudes in the North Atlantic, suggesting marine populations persisted through cycles of glaciation and are potentially adapted to local environments. Here, whole-genome sequencing was used to test whether North Atlantic marine coastal populations of the kelp Alaria esculenta survived in the area of southwestern Greenland during the Last Glacial Maximum. We present the first annotated genome for A. esculenta and call variant positions in 54 individuals from populations in Atlantic Canada, Greenland, Faroe Islands, Norway and Ireland. Differentiation across populations was reflected in ~1.9 million single nucleotide polymorphisms, which further revealed mixed ancestry in the Faroe Islands individuals between putative Greenlandic and European lineages. Time-calibrated organellar phylogenies suggested Greenlandic populations were established during the last interglacial period more than 100,000 years ago, and that the Faroe Islands population was probably established following the Last Glacial Maximum. Patterns in population statistics, including nucleotide diversity, minor allele frequencies, heterozygosity and linkage disequilibrium decay, nonetheless suggested glaciation reduced Canadian Atlantic and Greenlandic populations to small effective sizes during the most recent glaciation. Functional differentiation was further reflected in exon read coverage, which revealed expansions unique to Greenland in 337 exons representing 162 genes, and a modest degree of exon loss (103 exons from 56 genes). Altogether, our genomic results provide strong evidence that A. esculenta populations were resilient to past climatic fluctuations related to glaciations and that high-latitude populations are potentially already adapted to local conditions as a result.
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Affiliation(s)
| | - Antoine Fort
- Plant Systems Biology Lab, Ryan Institute, SFI MaREI Centre for Climate, Energy and Marine, School of Natural SciencesNational University of Ireland GalwayGalwayIreland
- Present address:
Department of Life and Physical SciencesAthlone Institute of TechnologyAthloneIreland
| | - Masami Inaba
- Plant Systems Biology Lab, Ryan Institute, SFI MaREI Centre for Climate, Energy and Marine, School of Natural SciencesNational University of Ireland GalwayGalwayIreland
| | - Ronan Sulpice
- Plant Systems Biology Lab, Ryan Institute, SFI MaREI Centre for Climate, Energy and Marine, School of Natural SciencesNational University of Ireland GalwayGalwayIreland
| | - Cliodhna Ní Ghriofa
- Business Development ManagerMarine Innovation Development Centre Páirc Na MaraGalwayIreland
| | | | - Karen Filbee‐Dexter
- School of Biological Sciences and UWA Oceans InstituteUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Christophe Vieira
- Kobe University Research Center for Inland SeasKobe UniversityKobeJapan
| | - Hiroshi Kawai
- Kobe University Research Center for Inland SeasKobe UniversityKobeJapan
| | - Takeaki Hanyuda
- School of Marine BiosciencesKitasato UniversitySagamiharaJapan
| | - Dorte Krause‐Jensen
- Department of EcoscienceAarhus UniversityAarhusDenmark
- Arctic Research CenterAarhus UniversityAarhusDenmark
| | | | - Samuel Starko
- Department of BiologyUniversity of VictoriaVictoriaCanada
| | - Heroen Verbruggen
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
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Bringloe TT, Wilkinson DP, Goldsmit J, Savoie AM, Filbee‐Dexter K, Macgregor KA, Howland KL, McKindsey CW, Verbruggen H. Arctic marine forest distribution models showcase potentially severe habitat losses for cryophilic species under climate change. GLOBAL CHANGE BIOLOGY 2022; 28:3711-3727. [PMID: 35212084 PMCID: PMC9314671 DOI: 10.1111/gcb.16142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 05/06/2023]
Abstract
The Arctic is among the fastest-warming areas of the globe. Understanding the impact of climate change on foundational Arctic marine species is needed to provide insight on ecological resilience at high latitudes. Marine forests, the underwater seascapes formed by seaweeds, are predicted to expand their ranges further north in the Arctic in a warmer climate. Here, we investigated whether northern habitat gains will compensate for losses at the southern range edge by modelling marine forest distributions according to three distribution categories: cryophilic (species restricted to the Arctic environment), cryotolerant (species with broad environmental preferences inclusive but not limited to the Arctic environment), and cryophobic (species restricted to temperate conditions) marine forests. Using stacked MaxEnt models, we predicted the current extent of suitable habitat for contemporary and future marine forests under Representative Concentration Pathway Scenarios of increasing emissions (2.6, 4.5, 6.0, and 8.5). Our analyses indicate that cryophilic marine forests are already ubiquitous in the north, and thus cannot expand their range under climate change, resulting in an overall loss of habitat due to severe southern range contractions. The extent of marine forests within the Arctic basin, however, is predicted to remain largely stable under climate change with notable exceptions in some areas, particularly in the Canadian Archipelago. Succession may occur where cryophilic and cryotolerant species are extirpated at their southern range edge, resulting in ecosystem shifts towards temperate regimes at mid to high latitudes, though many aspects of these shifts, such as total biomass and depth range, remain to be field validated. Our results provide the first global synthesis of predicted changes to pan-Arctic coastal marine forest ecosystems under climate change and suggest ecosystem transitions are unavoidable now for some areas.
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Affiliation(s)
| | | | - Jesica Goldsmit
- Fisheries and Oceans CanadaArctic and Aquatic Research DivisionWinnipegManitobaCanada
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuébecCanada
| | - Amanda M. Savoie
- Centre for Arctic Knowledge and ExplorationCanadian Museum of NatureOttawaOntarioCanada
| | - Karen Filbee‐Dexter
- Département de BiologieArcticNetQuébec OcéanUniversité LavalQuébecQuébecCanada
- School of Biological SciencesUWA Oceans InstituteUniversity of Western AustraliaCrawleyWestern AustraliaAustralia
- Institute of Marine ResearchFloedivigen Research StationHisNorway
| | | | - Kimberly L. Howland
- Fisheries and Oceans CanadaArctic and Aquatic Research DivisionWinnipegManitobaCanada
| | | | - Heroen Verbruggen
- School of BioSciencesUniversity of MelbourneMelbourneVictoriaAustralia
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Draper I, Villaverde T, Garilleti R, Burleigh JG, McDaniel SF, Mazimpaka V, Calleja JA, Lara F. An NGS-Based Phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) With the Proposal of the New Genus Rehubryum From Zealandia. FRONTIERS IN PLANT SCIENCE 2022; 13:882960. [PMID: 35646035 PMCID: PMC9133926 DOI: 10.3389/fpls.2022.882960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Phylogenomic data increase the possibilities of resolving the evolutionary and systematic relationships among taxa. This is especially valuable in groups with few and homoplasious morphological characters, in which systematic and taxonomical delimitations have been traditionally difficult. Such is the case of several lineages within Bryophyta, like Orthotrichaceae, the second most diverse family of mosses. Members of tribe Orthotricheae are common in temperate and cold regions, as well as in high tropical mountains. In extratropical areas, they represent one of the main components of epiphytic communities, both in dry and oceanic or hyperoceanic conditions. The epiphytic environment is considered a hostile one for plant development, mainly due to its low capacity of moisture retention. Thus, the diversification of the Orthotrichaceae in this environment could be seen as striking. Over the last two decades, great taxonomic and systematic progresses have led to a rearrangement at the generic level in this tribe, providing a new framework to link environment to patterns of diversification. Here, we use nuclear loci targeted with the GoFlag 408 enrichment probe set to generate a well-sampled phylogeny with well-supported suprageneric taxa and increasing the phylogenetic resolution within the two recognized subtribes. Specifically, we show that several genera with Ulota-like morphology jointly constitute an independent lineage. Within this lineage, the recently described Atlantichella from Macaronesia and Western Europe appears as the sister group of Ulota bellii from Zealandia. This latter species is here segregated in the new genus Rehubryum. Assessment of the ecological and biogeographical affinities of the species within the phylogenetic framework suggests that niche adaptation (including climate and substrate) may be a key evolutionary driver that shaped the high diversification of Orthotricheae.
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Affiliation(s)
- Isabel Draper
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Tamara Villaverde
- Departamento de Biodiversidad, Ecología y Evolución,Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Biología, Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Ricardo Garilleti
- Departamento de Botánica y Geología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
| | - J. Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Stuart F. McDaniel
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Vicente Mazimpaka
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan A. Calleja
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco Lara
- Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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