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Sexton JP, Clemens M, Bell N, Hall J, Fyfe V, Hoffmann AA. Patterns and effects of gene flow on adaptation across spatial scales: implications for management. J Evol Biol 2024; 37:732-745. [PMID: 38888218 DOI: 10.1093/jeb/voae064] [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: 09/16/2023] [Revised: 03/21/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.
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Affiliation(s)
- Jason P Sexton
- Department of Life and Environmental Sciences, University of California, Merced, CA, United States
| | - Molly Clemens
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Nicholas Bell
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Joseph Hall
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Verity Fyfe
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Ary A Hoffmann
- Pest and Environmental Adaptation Research Group, Bio21 Institute, School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
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Mahdavikia F, Ebadi MT, Shojaeiyan A, Ayyari M, Falahati-Anbaran M. Genetic variation and structure of endemic and endangered wild celery ( Kelussia odoratissima Mozaff.) quantified using novel microsatellite markers developed by next-generation sequencing. FRONTIERS IN PLANT SCIENCE 2024; 15:1301936. [PMID: 38638345 PMCID: PMC11024376 DOI: 10.3389/fpls.2024.1301936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/29/2024] [Indexed: 04/20/2024]
Abstract
Kelussia odoratissima Mozaff. (Apiaceae) is a native plant that has been traditionally consumed in Iran's food and pharmaceutical industries. Overharvesting of the taxon, especially at the beginning of the growing season, due to its considerable medicinal and economic value, is believed to be the main reason for the extirpating of this plant. The consequences of the severe anthropogenic impacts on the genetic diversity of populations are poorly known. In order to investigate the level of genetic variation and patterns of the genetic structure of K. odoratissima, we developed novel microsatellite markers using the 454 Roche next-generation sequencing (NGS) platform for the first time. Out of 1,165 microsatellite markers bioinformatically confirmed, twenty-five were tested, of which 23 were used to screen genetic variation across 12 natural populations. Our results showed that the average number of alleles per locus and the polymorphic information content (PIC) were 10.87 (range 7 to 27), and 0.81 (range 0.67 to 0.94), respectively. The mean observed and expected heterozygosities (± SD) across all populations were 0.80 ± 0.31 and 0.72 ± 0.14, respectively. The average pairwise FST among the populations was 0.37 (range 0.04 to 0.81). Bayesian and distance-based clustering, and principal coordinate analyses revealed at least four major genetic clusters. Although high level of structure can be explained by landscape topography and geographic distance, presence of admixed populations can be associated to seed or pollen dispersal. Contrary to expectations, the high level of genetic variation and lack of inbreeding suggest that overexploitation has not yet significantly purged the allelic variability within the natural populations in protected areas.
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Affiliation(s)
- Faezeh Mahdavikia
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Mohammad-Taghi Ebadi
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Abdolali Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Mahdi Ayyari
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Mohsen Falahati-Anbaran
- NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Habibi N, Al Salameen F, Vyas N, Rahman M, Kumar V, Shajan A, Zakir F, Razzack NA, Al Doaij B. Genome survey and genetic characterization of Acacia pachyceras O. Schwartz. FRONTIERS IN PLANT SCIENCE 2023; 14:1062401. [PMID: 36875582 PMCID: PMC9979705 DOI: 10.3389/fpls.2023.1062401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Acacia pachyceras O. Schwartz (Leguminoseae), a woody tree growing in Kuwait is critically endangered. High throughput genomic research is immediately needed to formulate effective conservation strategies for its rehabilitation. We therefore, performed a genome survey analysis of the species. Whole genome sequencing generated ~97 Gb of raw reads (92x coverage) with a per base quality score above Q30. The k-mer analysis (17 mer) revealed its genome to be 720Mb in size with an average guanine-cytosine (GC) ratio of 35%. The assembled genome was analyzed for repeat regions (45.4%-interspersed repeats; 9%-retroelements; 2%-DNA transposons). BUSCO assessment of completeness of genome identified 93% of assembly to be complete. Gene alignments in BRAKER2 yielded 34,374 transcripts corresponding to 33,650 genes. Average length of coding sequences and protein sequences were recorded as 1,027nts and 342aa, respectively. GMATA software filtered a total of 901,755 simple sequence repeats (SSRs) regions against which 11,181 unique primers were designed. A subset of 110 SSR primers were PCR validated and demonstrated for its application in genetic diversity analysis of Acacia. The SSR primers successfully amplified A. gerrardii seedlings DNA depicting cross transferability among species. The principal coordinate analysis and the split decomposition tree (bootstrapping runs of 1000 replicates) distributed the Acacia genotypes into two clusters. The flow cytometry analysis revealed the A. pachyceras genome to be polyploid (6x). The DNA content was predicted as 2.46 pg, 1.23 pg, and 0.41 pg corresponding to 2C DNA, 1C DNA and 1Cx DNA, respectively. The results provide a base for further high throughput genomic studies and molecular breeding for its conservation.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Fadila Al Salameen
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Nishant Vyas
- Department of Immunology, Logical Life Sciences, Pune, India
| | - Muhammad Rahman
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Vinod Kumar
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Anisha Shajan
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Farhana Zakir
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
| | - Bashayer Al Doaij
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Kuwait, Kuwait
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Hodgson RJ, Liddicoat C, Cando‐Dumancela C, Blyth C, Watson CD, Breed MF. Local and non‐local soil microbiota impede germination of the endangered
Acacia whibleyana. AUSTRAL ECOL 2023. [DOI: 10.1111/aec.13275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Riley J. Hodgson
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Craig Liddicoat
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
- School of Public Health University of Adelaide Adelaide South Australia Australia
| | | | - Colette Blyth
- School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Carl D. Watson
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
| | - Martin F. Breed
- College of Science and Engineering Flinders University Bedford Park South Australia Australia
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McLay TGB, Murphy DJ, Holmes GD, Mathews S, Brown GK, Cantrill DJ, Udovicic F, Allnutt TR, Jackson CJ. A genome resource for Acacia, Australia's largest plant genus. PLoS One 2022; 17:e0274267. [PMID: 36240205 PMCID: PMC9565413 DOI: 10.1371/journal.pone.0274267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022] Open
Abstract
Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes.
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Affiliation(s)
- Todd G. B. McLay
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Gareth D. Holmes
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Sarah Mathews
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Gillian K. Brown
- Queensland Herbarium, Department of Environment and Science, Toowong, Queensland, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | | | - Chris J. Jackson
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
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Brooks E, Slender AL, Cu S, Breed MF, Stangoulis JCR. A range-wide analysis of population structure and genomic variation within the critically endangered spiny daisy (Acanthocladium dockeri). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01468-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractUnderstanding population structure and genetic diversity is important for designing effective conservation strategies. As a critically endangered shrub, the six remaining extant populations of spiny daisy (Acanthocladium dockeri) are restricted to country roadsides in the mid-north of South Australia, where the species faces many ongoing abiotic and biotic threats to survival. Currently the spiny daisy is managed by selecting individuals from the extant populations and translocating them to establish insurance populations. However, there is little information available on the genetic differentiation between populations and diversity within source populations, which are essential components of planning translocations. To help fill this knowledge gap, we analysed population structure within and among all six of its known wild populations using 7,742 SNPs generated by a genotyping-by-sequencing approach. Results indicated that each population was strongly differentiated, had low levels of genetic diversity, and there was no evidence of inter-population gene flow. Individuals within each population were generally closely related, however, the Melrose population consisted entirely of clones. Our results suggest genetic rescue should be applied to wild spiny daisy populations to increase genetic diversity that will subsequently lead to greater intra-population fitness and adaptability. As a starting point, we suggest focussing on improving seed viability via inter-population crosses such as through hand pollination experiments to experimentally assess their sexual compatibility with the hope of increasing spiny daisy sexual reproduction and long-term reproductive fitness.
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Habibi N, Salameen FA, Rahman M, Shajan A, Zakir F, Abdulrazzack N. Comparison and Optimization of DNA Isolation Protocols for High Throughput Genomic Studies of Acacia pachyceras Schwartz. MethodsX 2022; 9:101799. [PMID: 35990814 PMCID: PMC9386096 DOI: 10.1016/j.mex.2022.101799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/22/2022] [Indexed: 11/10/2022] Open
Abstract
We describe the optimization and validation of six DNA isolation protocols from fresh leaves of the rare tree Acacia pachyceras. The first four protocols employed three commercial kits (Sigma, Nucleospin1, Nucleospin 2, Promega) whereas the remaining two were based on the traditional sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide CTAB methods. Each protocol provided significantly different results concerning DNA concentration (p < 0.032), yield (p < 0.000), contaminant carry over, protocol duration, cost per sample, and comprehensive cost. We demonstrated the applicability of all the tested protocols in DNA barcoding. The protocol yielded maximum amounts (92.85 µg) of DNA in a rapid turnaround time (8 h). The quantity and purity surpassed all the other tested methods. DNA extracted by the CTAB method was the best for NGS (Phred score >Q30). These protocols will be useful tools for molecular research of Acacia pachyceras and other closely related tree species.
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Draft genome sequence and SSR mining data of Acacia pachyceras Schwartz. Data Brief 2022; 42:108031. [PMID: 35313494 PMCID: PMC8933827 DOI: 10.1016/j.dib.2022.108031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 11/22/2022] Open
Abstract
Acacia tree population is declining in several countries of the world especially in the Arabian peninsula due to human-induced activities. The tree has potential medicinal and economic benefits as a source of fuel and timber. It can fix nitrogen, a significant property that assists in desert rehabilitation. However, the lack of genomic information of Acacia pachyceras hampers its genetic study and breeding process. We performed paired-end sequencing of A. pachyceras at a depth of 120X to obtain raw sequences of 108.9 GB with a per base quality >Q30. Filtered raw data was assembled into a fasta file of 4 GB. The assembled genomic sequences consisted of 901,755 single sequence repeats (SSRs). In total 11,596 primer pairs were designed against these SSR motifs. The data generated provides baseline genomic information about the species and formulates a base for further sequencing of A. pachyceras through PACBio and HiC technologies. The novel developed SSR markers will facilitate genetic diversity and conservation studies for Acacia species.
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Bairu MW, Amelework AB, Coetzer WG. Genetic diversity and population structure of six South African Acacia mearnsii breeding populations based on SSR markers. JOURNAL OF PLANT RESEARCH 2021; 134:1243-1252. [PMID: 34302570 DOI: 10.1007/s10265-021-01331-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Black wattle (Acacia mearnsii) has great economic value as a commercial source of tannins, timber and a source of firewood for local and international markets. It has been suggested that to maximize the genetic gain of A. mearnsii plantations in South Africa, the gene pool that exist within ICFR needs to be broadened via introduction of new genotypes with diverse traits. In this work, 282 A. mearnsii samples sourced from the ICFR breeding program were genotyped using 11 cross-species SSR markers. Our results showed low to moderate genetic differentiation (FST) among the six breeding subpopulations, with positive inbreeding (FIS) values that could be attributed to an historical inbreeding event. Low levels of relatedness could however indicate some mechanism of inbreeding avoidance. The effects from a recent supplementation of genetic material from two native Australian populations were observed through genetic structuring analyses. Analysis of molecular variance (AMOVA) revealed that significant genetic variation was mainly distributed within populations (75%) and among individuals (23%). The results provide significant information on A. mearnsii population genetic diversity and structure, which can be used for conservation of the current subpopulations and future tree improvement programs.
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Affiliation(s)
- Michael W Bairu
- Institute for Commercial Forestry Research (ICFR), P. O. Box 100281, Scottsville, 3209, South Africa
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria, 0001, South Africa
| | - Assefa B Amelework
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria, 0001, South Africa
| | - Willem G Coetzer
- Institute for Commercial Forestry Research (ICFR), P. O. Box 100281, Scottsville, 3209, South Africa.
- Department of Genetics, University of the Free State, P. O. Box 339, Bloemfontein, 9300, South Africa.
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Blyth C, Christmas MJ, Bickerton DC, Breed MF, Foster NR, Guerin GR, Mason ARG, Lowe AJ. Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy. Life (Basel) 2021; 11:553. [PMID: 34208381 PMCID: PMC8231295 DOI: 10.3390/life11060553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.
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Affiliation(s)
- Colette Blyth
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | | | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Nicole R. Foster
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Greg R. Guerin
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- Terrestrial Ecosystem Research Network (TERN), University of Adelaide, Adelaide 5005, Australia
| | - Alex R. G. Mason
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Andrew J. Lowe
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
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