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Blommaert J, Sandoval-Castillo J, Beheregaray LB, Wellenreuther M. Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper. Genomics 2024; 116:110929. [PMID: 39216708 DOI: 10.1016/j.ygeno.2024.110929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.
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Affiliation(s)
- Julie Blommaert
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand.
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research, Nelson, New Zealand; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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2
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Papa Y, Wellenreuther M, Morrison MA, Ritchie PA. Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus). G3 (BETHESDA, MD.) 2022; 13:6883520. [PMID: 36477875 PMCID: PMC9911067 DOI: 10.1093/g3journal/jkac315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022]
Abstract
Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
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Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand,School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Mark A Morrison
- National Institute of Water and Atmospheric Research, Auckland 1010, New Zealand
| | - Peter A Ritchie
- Corresponding author: Te Toki A Rata, Gate 7, Kelburn Parade, Wellington 6012, New Zealand.
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3
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Marchessaux G, Lüskow F, Bejean M, Pakhomov EA. Increasing Temperature Facilitates Polyp Spreading and Medusa Appearance of the Invasive Hydrozoan Craspedacusta sowerbii. BIOLOGY 2022; 11:biology11081100. [PMID: 35892956 PMCID: PMC9331908 DOI: 10.3390/biology11081100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/05/2022]
Abstract
The freshwater jellyfish Craspedacusta sowerbii is among the most widespread invasive species, observed across a wide temperature range. The aim of this study is to analyze the polyp and medusa stages response to different temperatures by using (i) an experimental study on the polyp colony growth at 19 and 29 °C, and (ii) prediction of the Thermal Habitat Suitability (THS) based on the thermal tolerance of the medusa stage. The total number of polyps and colonies was greater at high temperature. At 19 °C, colonies with 1 to 5 polyps were present, with colonies of 1 to 3 polyps numerically dominating. At 29 °C, colonies were 80% composed of 1- to 2-polyps. Based on the published medusa pulsation rhythm data, a Thermal Performance Curve (TPC) regression was performed and used to monthly predict the THS for current and future (2050 and 2100) scenarios. The southern hemisphere offered optimal conditions (THS > 0.6) year-round. In the northern hemisphere, the optimum period was predicted to be between June and September. The future THS were considerably larger than at present with an increase in optimal THS at higher latitudes (up to 60° N). The combination of experimental and modeling approaches allows to identify the optimal thermal conditions of the polyp and medusa stages and to predict their invasive capacities.
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Affiliation(s)
- Guillaume Marchessaux
- Department of Earth and Marine Science, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
- Correspondence:
| | - Florian Lüskow
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2039-2207 Main Mall, Vancouver, BC V6T 1Z4, Canada; (F.L.); (E.A.P.)
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Mickaël Bejean
- Muséum de Besançon, 99 Rue Des Fusillés, La Citadelle, 25000 Besançon, France;
| | - Evgeny A. Pakhomov
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2039-2207 Main Mall, Vancouver, BC V6T 1Z4, Canada; (F.L.); (E.A.P.)
- Institute for the Oceans and Fisheries, University of British Columbia, 2202 Main Mall, Vancouver, BC V6T 1Z4, Canada
- Hakai Institute, Heriot Bay, BC V0P 1H0, Canada
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Gervais CR, Champion C, Pecl GT. Species on the move around the Australian coastline: A continental-scale review of climate-driven species redistribution in marine systems. GLOBAL CHANGE BIOLOGY 2021; 27:3200-3217. [PMID: 33835618 PMCID: PMC8251616 DOI: 10.1111/gcb.15634] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/23/2021] [Indexed: 05/02/2023]
Abstract
Climate-driven changes in the distribution of species are a pervasive and accelerating impact of climate change, and despite increasing research effort in this rapidly emerging field, much remains unknown or poorly understood. We lack a holistic understanding of patterns and processes at local, regional and global scales, with detailed explorations of range shifts in the southern hemisphere particularly under-represented. Australian waters encompass the world's third largest marine jurisdiction, extending from tropical to sub-Antarctic climate zones, and have waters warming at rates twice the global average in the north and two to four times in the south. Here, we report the results of a multi-taxon continent-wide review describing observed and predicted species redistribution around the Australian coastline, and highlight critical gaps in knowledge impeding our understanding of, and response to, these considerable changes. Since range shifts were first reported in the region in 2003, 198 species from nine Phyla have been documented shifting their distribution, 87.3% of which are shifting poleward. However, there is little standardization of methods or metrics reported in observed or predicted shifts, and both are hindered by a lack of baseline data. Our results demonstrate the importance of historical data sets and underwater visual surveys, and also highlight that approximately one-fifth of studies incorporated citizen science. These findings emphasize the important role the public has had, and can continue to play, in understanding the impact of climate change. Most documented shifts are of coastal fish species in sub-tropical and temperate systems, while tropical systems in general were poorly explored. Moreover, most distributional changes are only described at the poleward boundary, with few studies considering changes at the warmer, equatorward range limit. Through identifying knowledge gaps and research limitations, this review highlights future opportunities for strategic research effort to improve the representation of Australian marine species and systems in climate-impact research.
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Affiliation(s)
- Connor R. Gervais
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Curtis Champion
- Fisheries ResearchNSW Department of Primary IndustriesCoffs HarbourNSWAustralia
- Southern Cross UniversityNational Marine Science CentreCoffs HarbourNSWAustralia
| | - Gretta T. Pecl
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTasAustralia
- Centre for Marine SocioecologyUniversity of TasmaniaHobartTasAustralia
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Mendes T, Gomes C, Monteiro N, Antunes A. Strong Sexual Selection Does Not Induce Population Differentiation in a Fish Species with High Dispersal Potential: The Curious Case of the Worm Pipefish Nerophis lumbriciformis (Teleostei: Syngnathidae). J Hered 2020; 111:585-592. [PMID: 33313855 DOI: 10.1093/jhered/esaa052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/05/2020] [Indexed: 11/13/2022] Open
Abstract
High levels of population differentiation are a common demographic pattern in syngnathids, even at small geographical scales. This is probably the end result of the common life history traits observed within the family, involving limited dispersal capabilities and strong habitat dependency. The worm pipefish, Nerophis lumbriciformis, which displays all these characteristics, also presents an additional variable potentially able to promote population differentiation: high sexual selection intensity, especially at the extremes of its distribution. Nevertheless, an early life pelagic stage, which presumably allows for admixture, could prevent population structuring. Here, we assessed the phylogeography of N. lumbriciformis through the amplification of the cytochrome b, 12S, and 16S rDNA mitochondrial markers as well as the rhodopsin nuclear marker, performed upon 119 individuals. We observed a genetically homogeneous population with indications of extensive gene flow. We tentatively attribute this finding to the dispersal potential of the species' pelagic larvae, supported by marine currents acting as major dispersal vectors. We also detected a signal of expansion towards the poles, consistent with the current climate change scenario. Despite the marked latitudinal differences in the phenotype of reproducing worm pipefish, the absence of clear population structuring suggests that phenotypic plasticity can have a significant role in the expression of sexual selection-related traits.
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Affiliation(s)
- Tito Mendes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
| | - Cidália Gomes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto, Portugal
| | - Nuno Monteiro
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal.,CIBIO (InBio), Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, Vairão, Portugal.,Faculdade de Ciências da Saúde, CEBIMED, Universidade Fernando Pessoa, Rua Carlos da Maia, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
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Ángeles-González LE, Lima FD, Caamal-Monsreal C, Díaz F, Rosas C. Exploring the effects of warming seas by using the optimal and pejus temperatures of the embryo of three Octopoda species in the Gulf of Mexico. J Therm Biol 2020; 94:102753. [PMID: 33292994 DOI: 10.1016/j.jtherbio.2020.102753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/10/2020] [Accepted: 10/05/2020] [Indexed: 11/27/2022]
Abstract
Using data related to thermal optimal and pejus of the embryos of Octopus americanus from Brazil and O. insularis and O. maya from Mexico, this study aimed to project the potential distribution areas in the Gulf of Mexico and predict distribution shifts under different Representative Concentration Pathway scenarios (RCP 6 and 8.5) for the years 2050 and 2100. The different thermal tolerances elicited different responses to current and future scenarios. In this sense, O. insularis and O. maya thermal niches stretch from the Caribbean to Florida. Nevertheless, O. insularis may inhabit warmer areas than O. maya. Surprisingly, no area was considered thermally habitable for O. americanus, which could have been associated with the use of data of populations thermally adapted to temperate conditions south of Brazil. According to models, a warming scenario would cause a restriction of the available thermal niche of O. maya, while O. insularis could expand under RCP 6 scenarios. This restriction was more substantial in the RCP 8.5 scenario. Nevertheless, under the RCP 8.5 scenario, the temperature in 2100 may negatively affect even O. insularis, the species most thermal tolerant. If our results are accurate, the fishing yield of O. insularis will increase in the future, replacing the heavily exploited O. maya in the coasts of the southern Gulf of Mexico. Regarding O. americanus, no inference might be made until thermal tolerances of locally adapted populations can be studied.
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Affiliation(s)
- Luis Enrique Ángeles-González
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, Coyoacán, Ciudad de México, 04510, Mexico; Laboratorio de Ecología Geográfica. Unidad de Conservación de la Biodiversidad, UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México (UNAM), Yucatán, Mexico; Universidad Nacional Autónoma de México, Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Laboratorio de Ecofisiología Aplicada, Puerto de Abrigo Sisal, Yucatán, 97356, Mexico; Laboratorio Nacional de Resiliencia Costera (CONACYT-Fac. de Ciencias, UNAM), Puerto de Abrigo, 97356 Sisal, Yucatán, Mexico
| | - Françoise D Lima
- Laboratory of Systematics and Evolutionary Ichthyology, Department of Botany and Zoology, Federal University of Rio Grande do Norte, 59078-900, Natal-RN, Brazil
| | - Claudia Caamal-Monsreal
- Universidad Nacional Autónoma de México, Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Laboratorio de Ecofisiología Aplicada, Puerto de Abrigo Sisal, Yucatán, 97356, Mexico
| | - Fernando Díaz
- Laboratorio de Ecofisiología de Organismos Acuáticos, Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Carlos Rosas
- Universidad Nacional Autónoma de México, Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Laboratorio de Ecofisiología Aplicada, Puerto de Abrigo Sisal, Yucatán, 97356, Mexico; Laboratorio Nacional de Resiliencia Costera (CONACYT-Fac. de Ciencias, UNAM), Puerto de Abrigo, 97356 Sisal, Yucatán, Mexico.
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7
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Briceño FA, Fitzgibbon QP, Polymeropoulos ET, Hinojosa IA, Pecl GT. Temperature alters the physiological response of spiny lobsters under predation risk. CONSERVATION PHYSIOLOGY 2020; 8:coaa065. [PMID: 32843966 PMCID: PMC7439581 DOI: 10.1093/conphys/coaa065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 04/19/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
Predation risk can strongly shape prey ecological traits, with specific anti-predator responses displayed to reduce encounters with predators. Key environmental drivers, such as temperature, can profoundly modulate prey energetic costs in ectotherms, although we currently lack knowledge of how both temperature and predation risk can challenge prey physiology and ecology. Such uncertainties in predator-prey interactions are particularly relevant for marine regions experiencing rapid environmental changes due to climate change. Using the octopus (Octopus maorum)-spiny lobster (Jasus edwardsii) interaction as a predator-prey model, we examined different metabolic traits of sub adult spiny lobsters under predation risk in combination with two thermal scenarios: 'current' (20°C) and 'warming' (23°C), based on projections of sea-surface temperature under climate change. We examined lobster standard metabolic rates to define the energetic requirements at specific temperatures. Routine metabolic rates (RMRs) within a respirometer were used as a proxy of lobster activity during night and day time, and active metabolic rates, aerobic scope and excess post-exercise oxygen consumption were used to assess the energetic costs associated with escape responses (i.e. tail-flipping) in both thermal scenarios. Lobster standard metabolic rate increased at 23°C, suggesting an elevated energetic requirement (39%) compared to 20°C. Unthreatened lobsters displayed a strong circadian pattern in RMR with higher rates during the night compared with the day, which were strongly magnified at 23°C. Once exposed to predation risk, lobsters at 20°C quickly reduced their RMR by ~29%, suggesting an immobility or 'freezing' response to avoid predators. Conversely, lobsters acclimated to 23°C did not display such an anti-predator response. These findings suggest that warmer temperatures may induce a change to the typical immobility predation risk response of lobsters. It is hypothesized that heightened energetic maintenance requirements at higher temperatures may act to override the normal predator-risk responses under climate-change scenarios.
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Affiliation(s)
- Felipe A Briceño
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania 7001, Australia
- Crustacean Ecophysiology Laboratory, Universidad Austral de Chile, Los Pinos s/n, Pelluco, Puerto Montt 5480000, Chile
| | - Quinn P Fitzgibbon
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Elias T Polymeropoulos
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Iván A Hinojosa
- Millennium Nucleus for Ecology and Sustainable Management of Oceanic Islands (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, 1781421, Chile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Facultad de Ciencias, Departamento de Ecología, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile
| | - Gretta T Pecl
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania 7001, Australia
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Against all odds: a tale of marine range expansion with maintenance of extremely high genetic diversity. Sci Rep 2020; 10:12707. [PMID: 32728141 PMCID: PMC7391780 DOI: 10.1038/s41598-020-69374-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
The displacement of species from equatorial latitudes to temperate locations following the increase in sea surface temperatures is among the significant reported consequences of climate change. Shifts in the distributional ranges of species result in fish communities tropicalisation, i.e., high latitude colonisations by typically low latitude distribution species. These movements create new interactions between species and new trophic assemblages. The Senegal seabream, Diplodus bellottii, may be used as a model to understand the population genetics of these invasions. In the last decades, this species has undergone an outstanding range expansion from its African area of origin to the Atlantic coast of the Iberian Peninsula, where now occurs abundantly. Mitochondrial and nuclear markers revealed a striking high haplotypic nucleotide and genetic diversity values, along with significant population differentiation throughout the present-day geographical range of the Senegal seabream. These results are not consistent with the central-marginal hypothesis, nor with the expectations of a leptokurtic distribution of individuals, as D. bellottii seems to be able to retain exceptional levels of diversity in marginal and recently colonised areas. We discuss possible causes for hyperdiversity and lack of geographical structure and subsequent implications for fisheries.
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9
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Papa Y, Oosting T, Valenza-Troubat N, Wellenreuther M, Ritchie PA. Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: an overview and outlook. NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1788612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Tom Oosting
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Noemie Valenza-Troubat
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
| | - Maren Wellenreuther
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Peter A. Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Banerjee AK, Hou Z, Lin Y, Lan W, Tan F, Xing F, Li G, Guo W, Huang Y. Going with the flow: analysis of population structure reveals high gene flow shaping invasion pattern and inducing range expansion of Mikania micrantha in Asia. ANNALS OF BOTANY 2020; 125:1113-1126. [PMID: 32173740 PMCID: PMC7262463 DOI: 10.1093/aob/mcaa044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. METHODS We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. KEY RESULTS We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. CONCLUSIONS These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.
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Affiliation(s)
- Achyut Kumar Banerjee
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuangwei Hou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuting Lin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wentao Lan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fengxiao Tan
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fen Xing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guanghe Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yelin Huang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- For correspondence. E-mail
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11
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Pecl GT, Ogier E, Jennings S, van Putten I, Crawford C, Fogarty H, Frusher S, Hobday AJ, Keane J, Lee E, MacLeod C, Mundy C, Stuart-Smith J, Tracey S. Autonomous adaptation to climate-driven change in marine biodiversity in a global marine hotspot. AMBIO 2019; 48:1498-1515. [PMID: 31098878 PMCID: PMC6883019 DOI: 10.1007/s13280-019-01186-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 02/01/2019] [Accepted: 04/09/2019] [Indexed: 05/05/2023]
Abstract
While governments and natural resource managers grapple with how to respond to climatic changes, many marine-dependent individuals, organisations and user-groups in fast-changing regions of the world are already adjusting their behaviour to accommodate these. However, we have little information on the nature of these autonomous adaptations that are being initiated by resource user-groups. The east coast of Tasmania, Australia, is one of the world's fastest warming marine regions with extensive climate-driven changes in biodiversity already observed. We present and compare examples of autonomous adaptations from marine users of the region to provide insights into factors that may have constrained or facilitated the available range of autonomous adaptation options and discuss potential interactions with governmental planned adaptations. We aim to support effective adaptation by identifying the suite of changes that marine users are making largely without government or management intervention, i.e. autonomous adaptations, to better understand these and their potential interactions with formal adaptation strategies.
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Affiliation(s)
- Gretta T. Pecl
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
| | - Emily Ogier
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
| | - Sarah Jennings
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
- Tasmanian School of Business and Economics, University of Tasmania, Private Bag 84, Hobart, TAS 7001 Australia
| | - Ingrid van Putten
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
- CSIRO Oceans and Atmosphere, 3-4 Castray Esplanade, Hobart, TAS 7004 Australia
| | - Christine Crawford
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
| | - Hannah Fogarty
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
| | - Stewart Frusher
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
| | - Alistair J. Hobday
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
- CSIRO Oceans and Atmosphere, 3-4 Castray Esplanade, Hobart, TAS 7004 Australia
| | - John Keane
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
| | - Emma Lee
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
- Centre for Social Impact at Swinburne University of Technology, Hawthorn, VIC 3122 Australia
| | - Catriona MacLeod
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
- Centre for Marine Socioecology, University of Tasmania, Private Bag 49, Hobart, TAS 7001 Australia
| | - Craig Mundy
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
| | - Jemina Stuart-Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
| | - Sean Tracey
- Institute for Marine and Antarctic Studies, University of Tasmania, PO Box 49, Hobart, TAS 7001 Australia
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12
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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13
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Donelson JM, Sunday JM, Figueira WF, Gaitán-Espitia JD, Hobday AJ, Johnson CR, Leis JM, Ling SD, Marshall D, Pandolfi JM, Pecl G, Rodgers GG, Booth DJ, Munday PL. Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180186. [PMID: 30966966 PMCID: PMC6365866 DOI: 10.1098/rstb.2018.0186] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
Climate change is leading to shifts in species geographical distributions, but populations are also probably adapting to environmental change at different rates across their range. Owing to a lack of natural and empirical data on the influence of phenotypic adaptation on range shifts of marine species, we provide a general conceptual model for understanding population responses to climate change that incorporates plasticity and adaptation to environmental change in marine ecosystems. We use this conceptual model to help inform where within the geographical range each mechanism will probably operate most strongly and explore the supporting evidence in species. We then expand the discussion from a single-species perspective to community-level responses and use the conceptual model to visualize and guide research into the important yet poorly understood processes of plasticity and adaptation. This article is part of the theme issue 'The role of plasticity in phenotypic adaptation to rapid environmental change'.
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Affiliation(s)
- Jennifer M. Donelson
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4810, Australia
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | | | - Will F. Figueira
- University of Sydney, School of Life and Environmental Sciences, Sydney 2006, Australia
| | - Juan Diego Gaitán-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, People's Republic of China
- CSIRO Oceans and Atmosphere, Hobart, Tasmania 7000, Australia
| | | | - Craig R. Johnson
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Jeffrey M. Leis
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7000, Australia
- Australian Museum Research Institute, Sydney, New South Wales 2001, Australia
| | - Scott D. Ling
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Dustin Marshall
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - John M. Pandolfi
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Gretta Pecl
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Giverny G. Rodgers
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4810, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - David J. Booth
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
| | - Philip L. Munday
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4810, Australia
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14
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Williamson CE, Neale PJ, Hylander S, Rose KC, Figueroa FL, Robinson SA, Häder DP, Wängberg SÅ, Worrest RC. The interactive effects of stratospheric ozone depletion, UV radiation, and climate change on aquatic ecosystems. Photochem Photobiol Sci 2019; 18:717-746. [DOI: 10.1039/c8pp90062k] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Summary of current knowledge about effects of UV radiation in inland and oceanic waters related to stratospheric ozone depletion and climate change.
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Affiliation(s)
| | | | - Samuel Hylander
- Centre for Ecology and Evolution in Microbial model Systems
- Linnaeus Univ
- Kalmar
- Sweden
| | - Kevin C. Rose
- Department of Biological Sciences
- Rensselaer Polytechnic Institute
- Troy
- USA
| | | | - Sharon A. Robinson
- Centre for Sustainable Ecosystem Solutions
- School of Earth
- Atmosphere and Life Sciences and Global Challenges Program
- University of Wollongong
- Australia
| | - Donat-P. Häder
- Department of Biology
- Friedrich-Alexander Universität
- Möhrendorf
- Germany
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